diff --git a/modules/lofreq/1.1/lofreq.smk b/modules/lofreq/1.1/lofreq.smk
index 5e60ab3f..4a8e57c2 100644
--- a/modules/lofreq/1.1/lofreq.smk
+++ b/modules/lofreq/1.1/lofreq.smk
@@ -15,7 +15,7 @@
 import oncopipe as op
 
 # Check that the oncopipe dependency is up-to-date. Add all the following lines to any module that uses new features in oncopipe
-min_oncopipe_version="1.0.11"
+min_oncopipe_version="1.0.12"
 import pkg_resources
 try:
     from packaging import version
@@ -58,6 +58,27 @@ localrules:
     _lofreq_all,
     _lofreq_link_to_preprocessed
 
+def _lofreq_get_capspace(wildcards):
+    CFG=config["lcr-modules"]["lofreq"]
+    default_bed = reference_files("genomes/{genome_build}/genome_fasta/main_chromosomes.bed")
+    if str(wildcards.seq_type) in CFG['switches']['regions_bed'].keys():
+        custom_bed = CFG['switches']['regions_bed'][wildcards.seq_type]
+    else:
+        custom_bed = default_bed
+    try:
+        if "tumour_id" in wildcards.keys():
+        # Get the appropriate capture space for this sample
+            this_bed = op.get_capture_space(CFG, wildcards.tumour_id, wildcards.genome_build, wildcards.seq_type, "bed")
+        else:
+            this_bed = op.get_capture_space(CFG, wildcards.normal_id, wildcards.genome_build, wildcards.seq_type, "bed")
+        this_bed = reference_files(this_bed)
+    except NameError:
+        # If we are using an older version of the reference workflow, use the same region file as the genome sample 
+        this_bed = custom_bed if custom_bed else default_bed
+    # If this is a genome sample, return a BED file listing all chromosomes
+    if wildcards.seq_type != "capture":
+        return custom_bed if custom_bed else default_bed
+    return this_bed
 
 ##### RULES #####
 
@@ -84,7 +105,7 @@ rule _lofreq_preprocess_normal:
         normal_bam = CFG["dirs"]["inputs"] + "bam/{seq_type}--{genome_build}/{normal_id}.bam",
         fasta = reference_files("genomes/{genome_build}/genome_fasta/genome.fa"),
         dbsnp = reference_files("genomes/{genome_build}/variation/dbsnp.common_all-151.vcf.gz"), #in our experience, this filter doesn't remove as many SNPs as one would expect
-        bed = op.switch_on_wildcard("seq_type", CFG["switches"]["regions_bed"])
+        bed = _lofreq_get_capspace
     output:
         preprocessing_start = CFG["dirs"]["lofreq_normal"] + "{seq_type}--{genome_build}/{normal_id}/preprocessing.started",
         vcf_relaxed = CFG["dirs"]["lofreq_normal"] + "{seq_type}--{genome_build}/{normal_id}/normal_relaxed.vcf.gz",
@@ -164,7 +185,7 @@ rule _lofreq_run_tumour_unmatched:
         vcf_relaxed = str(rules._lofreq_link_to_preprocessed.output.vcf_relaxed),
         fasta = reference_files("genomes/{genome_build}/genome_fasta/genome.fa"),
         dbsnp = reference_files("genomes/{genome_build}/variation/dbsnp.common_all-151.vcf.gz"), #in our experience, this filter doesn't remove as many SNPs as one would expect
-        bed = op.switch_on_wildcard("seq_type", CFG["switches"]["regions_bed"])
+        bed = _lofreq_get_capspace
     output:
         vcf_snvs_filtered = CFG["dirs"]["lofreq_somatic"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/somatic_final_minus-dbsnp.snvs.vcf.gz",
         vcf_indels_filtered = CFG["dirs"]["lofreq_somatic"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/somatic_final_minus-dbsnp.indels.vcf.gz",
@@ -202,7 +223,7 @@ rule _lofreq_run_tumour_matched:
         normal_bam = CFG["dirs"]["inputs"] + "bam/{seq_type}--{genome_build}/{normal_id}.bam",
         fasta = reference_files("genomes/{genome_build}/genome_fasta/genome.fa"),
         dbsnp = reference_files("genomes/{genome_build}/variation/dbsnp.common_all-151.vcf.gz"), #in our experience, this filter doesn't remove as many SNPs as one would expect
-        bed = op.switch_on_wildcard("seq_type", CFG["switches"]["regions_bed"])
+        bed = _lofreq_get_capspace
     output:
         vcf_relaxed = temp(CFG["dirs"]["lofreq_somatic"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/normal_relaxed.vcf.gz"),
         vcf_snvs_filtered = temp(CFG["dirs"]["lofreq_somatic"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/somatic_final_minus-dbsnp.snvs.vcf.gz"),
diff --git a/modules/manta/2.3/manta.smk b/modules/manta/2.3/manta.smk
index 41f33b1a..3a84e077 100644
--- a/modules/manta/2.3/manta.smk
+++ b/modules/manta/2.3/manta.smk
@@ -6,7 +6,7 @@
 
 # Original Snakefile Author:    Bruno Grande
 # Module Author:                Bruno Grande
-# Additional Contributors:      N/A
+# Additional Contributors:      Chris Rushton
 
 
 ##### SETUP #####
@@ -15,7 +15,7 @@
 import oncopipe as op
 
 # Check that the oncopipe dependency is up-to-date. Add all the following lines to any module that uses new features in oncopipe
-min_oncopipe_version="1.0.11"
+min_oncopipe_version="1.0.12"
 import pkg_resources
 try:
     from packaging import version
@@ -86,6 +86,20 @@ rule _manta_index_bed:
         tabix {output.bedz}
         """)
 
+def _manta_get_capspace(wildcards):
+    CFG = config["lcr-modules"]["manta"]
+    try:
+        # Get the appropriate capture space for this sample
+        this_bed = op.get_capture_space(CFG, wildcards.tumour_id, wildcards.genome_build, wildcards.seq_type, "bed.gz")
+        this_bed = reference_files(this_bed)
+    except NameError:
+        # If we are using an older version of the reference workflow, use the same region file as the genome sample
+        this_bed = str(config["lcr-modules"]["manta"]["dirs"]["chrom_bed"] + "{genome_build}.main_chroms.bed.gz")
+    # If this is a genome sample, return a BED file listing all chromosomes
+    if wildcards.seq_type != "capture":
+        this_bed = str(config["lcr-modules"]["manta"]["dirs"]["chrom_bed"] + "{genome_build}.main_chroms.bed.gz")
+    return this_bed
+
 # Configures the manta workflow with the input BAM files and reference FASTA file.
 rule _manta_configure_paired:
     input:
@@ -93,7 +107,7 @@ rule _manta_configure_paired:
         normal_bam = CFG["dirs"]["inputs"] + "bam/{seq_type}--{genome_build}/{normal_id}.bam",
         fasta = reference_files("genomes/{genome_build}/genome_fasta/genome.fa"),
         config = op.switch_on_wildcard("seq_type", CFG["switches"]["manta_config"]),
-        bedz = str(rules._manta_index_bed.output.bedz)
+        bedz = _manta_get_capspace
     output:
         runwf = CFG["dirs"]["manta"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/runWorkflow.py"
     log:
@@ -120,7 +134,7 @@ rule _manta_configure_unpaired:
         tumour_bam = CFG["dirs"]["inputs"] + "bam/{seq_type}--{genome_build}/{tumour_id}.bam",
         fasta = reference_files("genomes/{genome_build}/genome_fasta/genome.fa"),
         config = op.switch_on_wildcard("seq_type", CFG["switches"]["manta_config"]),
-        bedz = str(rules._manta_index_bed.output.bedz)
+        bedz = _manta_get_capspace
     output:
         runwf = CFG["dirs"]["manta"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/runWorkflow.py"
     log:
@@ -135,7 +149,7 @@ rule _manta_configure_unpaired:
         CFG["conda_envs"]["manta"]
     shell:
         op.as_one_line("""
-        configManta.py {params.opts} --referenceFasta {input.fasta} --callRegions {input.bedz}
+        configManta.py {params.opts} --referenceFasta {input.fasta} --callRegions {params.bedz}
         --runDir "$(dirname {output.runwf})" {params.tumour_bam_arg_name} {input.tumour_bam}
         --config {input.config} > {log.stdout} 2> {log.stderr}
         """)
@@ -291,6 +305,7 @@ def _manta_predict_output(wildcards):
     return outputs_with_bedpe + outputs_without_bedpe
 
 
+
 # Generates the target symlinks for each run depending on the Manta output VCF files
 rule _manta_dispatch:
     input:
diff --git a/modules/mutect2/2.0/mutect2.smk b/modules/mutect2/2.0/mutect2.smk
index 7b88b919..cdf0c5af 100644
--- a/modules/mutect2/2.0/mutect2.smk
+++ b/modules/mutect2/2.0/mutect2.smk
@@ -15,9 +15,10 @@
 # Import package with useful functions for developing analysis modules
 import oncopipe as op
 import inspect
+import pandas as pd
 
 # Check that the oncopipe dependency is up-to-date. Add all the following lines to any module that uses new features in oncopipe
-min_oncopipe_version="1.0.11"
+min_oncopipe_version="1.0.12"
 import pkg_resources
 try:
     from packaging import version
@@ -74,7 +75,20 @@ localrules:
 
 
 ##### RULES #####
-
+def _mutect_get_capspace(wildcards):
+    CFG = config["lcr-modules"]["mutect2"]
+    try:
+        # Get the appropriate capture space for this sample
+        cap_space = op.get_capture_space(CFG, wildcards.tumour_id, wildcards.genome_build, wildcards.seq_type, "interval_list")
+        cap_space = reference_files(cap_space)
+        this_space = cap_space
+    # If we are using an older version of the reference workflow, we don't need to do anything
+    except NameError:
+        this_space = reference_files("genomes/{genome_build}/genome_fasta/main_chromosomes.bed")
+    # If this isn't a capture sample, we don't have a capture space, so return nothing
+    if wildcards.seq_type != "capture":
+        this_space = reference_files("genomes/{genome_build}/genome_fasta/main_chromosomes.bed")
+    return this_space
 
 # Symlinks the input files into the module results directory (under '00-inputs/')
 rule _mutect2_input_bam:
@@ -97,11 +111,27 @@ rule _mutect2_dummy_positions:
 # Symlink chromosomes used for parallelization
 checkpoint _mutect2_input_chrs:
     input:
-        chrs = reference_files("genomes/{genome_build}/genome_fasta/main_chromosomes.txt")
+        candidate_positions = CFG["inputs"]["candidate_positions"] if CFG["inputs"]["candidate_positions"] else str(rules._mutect2_dummy_positions.output),
+        chrs = reference_files("genomes/{genome_build}/genome_fasta/main_chromosomes.txt"),
+        capture_arg = _mutect_get_capspace
     output:
-        chrs = CFG["dirs"]["inputs"] + "chroms/{genome_build}/main_chromosomes.txt"
+        chrs = CFG["dirs"]["inputs"] + "chroms/{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/mutated_chromosomes.txt"
     run:
-        op.absolute_symlink(input.chrs, output.chrs)
+        # obtain list of main chromosomes
+        main_chrs = pd.read_csv(input.chrs, comment='#', sep='\t', header=None)
+        main_chrs = main_chrs.iloc[:, 0].astype(str).unique().tolist()
+        #obtain list of chromosomes in candidate positions
+        candidate_chrs = pd.read_csv(input.candidate_positions, comment='#', sep='\t')
+        candidate_chrs = candidate_chrs.iloc[:, 0].astype(str).unique().tolist()
+        # obtain list of chromosomes in the capture space
+        interval_chrs = pd.read_csv(input.capture_arg, comment='@', sep='\t')
+        interval_chrs = interval_chrs.iloc[:, 0].astype(str).unique().tolist()
+        # intersect the three lists to obtain chromosomes present in all
+        intersect_chrs = list(set(main_chrs) & set(candidate_chrs) & set(interval_chrs))
+        # convert list to single-column df
+        intersect_chrs = pd.DataFrame(intersect_chrs).sort_values(0)
+        # write out the file with mutated chromosomes
+        intersect_chrs.to_csv(output.chrs, index=False, header=False)
 
 
 # Retrieves from SM tag from BAM and writes to file
@@ -123,13 +153,13 @@ rule _mutect2_get_sm:
 # The first function loads the wildcard-containing file path and additional args from the config. 
 # The second replaces wildcards with those used in the rule. 
 def _mutect2_get_interval_cli_arg(
-    vcf_in = config["lcr-modules"]["mutect2"]["inputs"]["candidate_positions"], 
+    vcf_in = config["lcr-modules"]["mutect2"]["inputs"]["candidate_positions"],
     interval_arg_in = config["lcr-modules"]["mutect2"]["options"]["mutect2_interval_rules"]
 ):
     def _mutect2_get_interval_cli_custom(wildcards, input):
         if vcf_in:
             param = f"-L {input.candidate_positions} {interval_arg_in}"
-        else: 
+        else:
             param = ""
         return param
     return _mutect2_get_interval_cli_custom
@@ -145,7 +175,8 @@ rule _mutect2_run_matched_unmatched:
         gnomad = reference_files("genomes/{genome_build}/variation/af-only-gnomad.{genome_build}.vcf.gz"),
         normal_sm = CFG["dirs"]["mutect2"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/{normal_id}_sm.txt", 
         pon = reference_files("genomes/{genome_build}/gatk/mutect2_pon.{genome_build}.vcf.gz"), 
-        candidate_positions = CFG["inputs"]["candidate_positions"] if CFG["inputs"]["candidate_positions"] else str(rules._mutect2_dummy_positions.output)
+        candidate_positions = CFG["inputs"]["candidate_positions"] if CFG["inputs"]["candidate_positions"] else str(rules._mutect2_dummy_positions.output),
+        capture_arg = _mutect_get_capspace
     output:
         vcf = temp(CFG["dirs"]["mutect2"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/chromosomes/{chrom}.output.vcf.gz"),
         tbi = temp(CFG["dirs"]["mutect2"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/chromosomes/{chrom}.output.vcf.gz.tbi"),
@@ -172,7 +203,7 @@ rule _mutect2_run_matched_unmatched:
         -I {input.tumour_bam} -I {input.normal_bam}
         -R {input.fasta} -normal "$(cat {input.normal_sm})" -O {output.vcf}
         --germline-resource {input.gnomad} 
-        -L {wildcards.chrom} {params.interval_arg} 
+        -L {wildcards.chrom} {params.interval_arg} -L {input.capture_arg}
         -pon {input.pon} --f1r2-tar-gz {output.f1r2}
         > {log.stdout} 2> {log.stderr}
         """)
@@ -186,7 +217,8 @@ rule _mutect2_run_no_normal:
         dict = reference_files("genomes/{genome_build}/genome_fasta/genome.dict"),
         gnomad = reference_files("genomes/{genome_build}/variation/af-only-gnomad.{genome_build}.vcf.gz"),
         pon = reference_files("genomes/{genome_build}/gatk/mutect2_pon.{genome_build}.vcf.gz"), 
-        candidate_positions = CFG["inputs"]["candidate_positions"] if CFG["inputs"]["candidate_positions"] else str(rules._mutect2_dummy_positions.output)
+        candidate_positions = CFG["inputs"]["candidate_positions"] if CFG["inputs"]["candidate_positions"] else str(rules._mutect2_dummy_positions.output),
+        capture_arg = _mutect_get_capspace
     output:
         vcf = temp(CFG["dirs"]["mutect2"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/chromosomes/{chrom}.output.vcf.gz"),
         tbi = temp(CFG["dirs"]["mutect2"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/chromosomes/{chrom}.output.vcf.gz.tbi"),
@@ -200,7 +232,7 @@ rule _mutect2_run_no_normal:
     params:
         mem_mb = lambda wildcards, resources: int(resources.mem_mb * 0.8),
         opts = CFG["options"]["mutect2_run"], 
-        interval_arg = _mutect2_get_interval_cli_arg() 
+        interval_arg = _mutect2_get_interval_cli_arg()
     conda:
         CFG["conda_envs"]["gatk"]
     threads:
@@ -212,7 +244,7 @@ rule _mutect2_run_no_normal:
         gatk Mutect2 --java-options "-Xmx{params.mem_mb}m" 
         {params.opts} -I {input.tumour_bam} -R {input.fasta} 
         -O {output.vcf} --germline-resource {input.gnomad} 
-        -L {wildcards.chrom} {params.interval_arg}
+        -L {wildcards.chrom} {params.interval_arg} -L {input.capture_arg}
         -pon {input.pon} --f1r2-tar-gz {output.f1r2}
         > {log.stdout} 2> {log.stderr}
         """)
diff --git a/modules/sage/1.0/sage.smk b/modules/sage/1.0/sage.smk
index 2fee054e..d48343b7 100644
--- a/modules/sage/1.0/sage.smk
+++ b/modules/sage/1.0/sage.smk
@@ -16,7 +16,7 @@
 import oncopipe as op
 
 # Check that the oncopipe dependency is up-to-date. Add all the following lines to any module that uses new features in oncopipe
-min_oncopipe_version="1.0.11"
+min_oncopipe_version="1.0.12"
 import pkg_resources
 try:
     from packaging import version
@@ -121,15 +121,29 @@ def get_chromosomes(wildcards):
     chromosomes= ",".join(chromosomes)    
     return chromosomes
 
+def _sage_get_capspace(wildcards):
+    CFG = config["lcr-modules"]["sage"]
+    try:
+        # Get the appropriate capture space for this sample
+        this_bed = op.get_capture_space(CFG, wildcards.tumour_id, wildcards.genome_build, wildcards.seq_type, "bed.gz")
+        this_bed = reference_files(this_bed)
+    except NameError:
+        # If we are using an older version of the reference workflow, use the same region file as the genome sample
+        this_bed = rules._download_sage_references.output.panel_bed
+    # If this is a genome sample, return a BED file listing all chromosomes
+    if wildcards.seq_type != "capture":
+        this_bed = rules._download_sage_references.output.panel_bed
+    return this_bed
+
 # Variant calling rule
 rule _run_sage:
     input:
         tumour_bam = CFG["dirs"]["inputs"] + "bam/{seq_type}--{genome_build}/{tumour_id}.bam",
         normal_bam = CFG["dirs"]["inputs"] + "bam/{seq_type}--{genome_build}/{normal_id}.bam",
         fasta = str(rules._input_references.output.genome_fa),
-        hotspots = str(rules._download_sage_references.output.hotspots),
-        panel_bed = str(rules._download_sage_references.output.panel_bed),
-        high_conf_bed = str(rules._download_sage_references.output.high_conf_bed)
+        hotspots = rules._download_sage_references.output.hotspots,
+        high_conf_bed = str(rules._download_sage_references.output.high_conf_bed),
+        panel_bed = _sage_get_capspace
     output:
         vcf = temp(CFG["dirs"]["sage"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/{tumour_id}--{normal_id}--{pair_status}.vcf"),
         vcf_gz = temp(CFG["dirs"]["sage"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/{tumour_id}--{normal_id}--{pair_status}.vcf.gz")
diff --git a/modules/strelka/1.1/strelka.smk b/modules/strelka/1.1/strelka.smk
index 5bebe48c..089fa085 100755
--- a/modules/strelka/1.1/strelka.smk
+++ b/modules/strelka/1.1/strelka.smk
@@ -16,7 +16,7 @@
 import oncopipe as op
 
 # Check that the oncopipe dependency is up-to-date. Add all the following lines to any module that uses new features in oncopipe
-min_oncopipe_version="1.0.11"
+min_oncopipe_version="1.0.12"
 import pkg_resources
 try:
     from packaging import version
@@ -53,10 +53,7 @@ localrules:
     _strelka_configure_unpaired,
     _strelka_filter_combine,
     _strelka_output_filtered_vcf,
-    _strelka_all,
-
-wildcard_constraints: 
-    var_type = "somatic.snvs|somatic.indels|variants"
+    _strelka_all
 
 ##### RULES #####
 
@@ -122,14 +119,29 @@ def _strelka_get_indel_cli_arg(vcf_in = config["lcr-modules"]["strelka"]["inputs
         return param
     return _strelka_get_indel_cli_custom
 
+def _strelka_get_capspace(wildcards):
+    CFG = config["lcr-modules"]["strelka"]
+    try:
+        # Get the appropriate capture space for this sample
+        this_bed = op.get_capture_space(CFG, wildcards.tumour_id, wildcards.genome_build, wildcards.seq_type, "bed.gz")
+        this_bed = reference_files(this_bed)
+    except NameError:
+        # If we are using an older version of the reference workflow, use the same region file as the genome sample
+        this_bed = str(config["lcr-modules"]["strelka"]["dirs"]["chrom_bed"] + "{genome_build}.main_chroms.bed.gz")
+    # If this is a genome sample, return a BED file listing all chromosomes
+    if wildcards.seq_type != "capture":
+        this_bed = str(config["lcr-modules"]["strelka"]["dirs"]["chrom_bed"] + "{genome_build}.main_chroms.bed.gz")
+
+    return this_bed
+
 
 rule _strelka_configure_paired: # Somatic
     input:
         tumour_bam = CFG["dirs"]["inputs"] + "bam/{seq_type}--{genome_build}/{tumour_id}.bam",
         normal_bam = CFG["dirs"]["inputs"] + "bam/{seq_type}--{genome_build}/{normal_id}.bam",
         fasta = reference_files("genomes/{genome_build}/genome_fasta/genome.fa"),
-        bedz = str(rules._strelka_index_bed.output.bedz),
-        indels = str(rules._strelka_input_vcf.output.vcf) if CFG["inputs"]["candidate_small_indels"] else str(rules._strelka_dummy_vcf.output)
+        indels = str(rules._strelka_input_vcf.output.vcf) if CFG["inputs"]["candidate_small_indels"] else str(rules._strelka_dummy_vcf.output),
+        bedz = _strelka_get_capspace
     output:
         runwf = CFG["dirs"]["strelka"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/runWorkflow.py"
     log:
@@ -137,7 +149,7 @@ rule _strelka_configure_paired: # Somatic
         stderr = CFG["logs"]["strelka"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/strelka_configure.stderr.log"
     params:
         indel_arg = _strelka_get_indel_cli_arg(),
-        opts = op.switch_on_wildcard("seq_type", CFG["options"]["configure"]),
+        opts = op.switch_on_wildcard("seq_type", CFG["options"]["configure"])
     wildcard_constraints:
         pair_status = "matched|unmatched"
     conda:
@@ -160,7 +172,7 @@ rule _strelka_configure_unpaired: # germline
     input:
         tumour_bam = CFG["dirs"]["inputs"] + "bam/{seq_type}--{genome_build}/{tumour_id}.bam",
         fasta = reference_files("genomes/{genome_build}/genome_fasta/genome.fa"),
-        bedz = str(rules._strelka_index_bed.output.bedz)
+        bedz = _strelka_get_capspace
     output:
         runwf = CFG["dirs"]["strelka"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/runWorkflow.py"
     log:
@@ -254,6 +266,8 @@ rule _strelka_filter_combine:
     log:
         stdout = CFG["logs"]["strelka"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/strelka_filter_combine.stdout.log",
         stderr = CFG["logs"]["strelka"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/strelka_filter_combine.stderr.log"
+    wildcard_constraints:
+        var_type = "somatic.snvs|somatic.indels|variants"
     shell:
         op.as_one_line("""
         bcftools concat -a {input.vcf} | 
@@ -276,6 +290,7 @@ def _strelka_get_output(wildcards):
         vcf = str(rules._strelka_filter_combine.output.vcf)
     return vcf
 
+
 # Symlinks the final output files into the module results directory (under '99-outputs/'). Links will always use "combined" in the name (dropping odd naming convention used by Strelka in unpaired mode)
 rule _strelka_output_filtered_vcf:
     input:
diff --git a/modules/vcf2maf/1.2/vcf2maf.smk b/modules/vcf2maf/1.2/vcf2maf.smk
index a53eee39..6d5e48b0 100644
--- a/modules/vcf2maf/1.2/vcf2maf.smk
+++ b/modules/vcf2maf/1.2/vcf2maf.smk
@@ -51,7 +51,7 @@ localrules:
     _vcf2maf_crossmap,
     _vcf2maf_all
 
-VERSION_MAP = {
+VCF2MAF_GENOME_VERSION_MAP = {
     "grch37": "GRCh37",
     "hg38": "GRCh38",
     "hs37d5": "GRCh37"
@@ -89,7 +89,7 @@ rule _vcf2maf_run:
         stderr = CFG["logs"]["vcf2maf"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/{base_name}_vcf2maf.stderr.log",
     params:
         opts = CFG["options"]["vcf2maf"],
-        build = lambda w: VERSION_MAP[w.genome_build],
+        build = lambda w: VCF2MAF_GENOME_VERSION_MAP[w.genome_build],
         custom_enst = op.switch_on_wildcard("genome_build", CFG["switches"]["custom_enst"])
     conda:
         CFG["conda_envs"]["vcf2maf"]
diff --git a/modules/vcf2maf/1.3/vcf2maf.smk b/modules/vcf2maf/1.3/vcf2maf.smk
index 17ba2f69..1cf2a63b 100644
--- a/modules/vcf2maf/1.3/vcf2maf.smk
+++ b/modules/vcf2maf/1.3/vcf2maf.smk
@@ -31,7 +31,7 @@ localrules:
     _vcf2maf_crossmap,
     _vcf2maf_all
 
-VERSION_MAP = {
+VCF2MAF_GENOME_VERSION_MAP = {
     "grch37": "GRCh37",
     "hg38": "GRCh38",
     "hs37d5": "GRCh37"
@@ -83,7 +83,7 @@ rule _vcf2maf_run:
         stderr = CFG["logs"]["vcf2maf"] + "{seq_type}--{genome_build}/{tumour_id}--{normal_id}--{pair_status}/{base_name}_vcf2maf.stderr.log",
     params:
         opts = CFG["options"]["vcf2maf"],
-        build = lambda w: VERSION_MAP[w.genome_build],
+        build = lambda w: VCF2MAF_GENOME_VERSION_MAP[w.genome_build],
         custom_enst = op.switch_on_wildcard("genome_build", CFG["switches"]["custom_enst"])
     conda:
         CFG["conda_envs"]["vcf2maf"]
@@ -115,7 +115,8 @@ rule _vcf2maf_run:
             --custom-enst {params.custom_enst}
             --retain-info gnomADg_AF
             >> {log.stdout} 2>> {log.stderr};
-        else echo "WARNING: PATH is not set properly, using $(which vcf2maf.pl) will result in error during execution. Please ensure $VCF2MAF_SCRIPT exists." > {log.stderr};fi
+        else echo "WARNING: PATH is not set properly, using $(which vcf2maf.pl) will result in error during execution. Please ensure $VCF2MAF_SCRIPT exists." > {log.stderr};fi  &&
+        touch {output.vep}
         """)
 
 rule _vcf2maf_gnomad_filter_maf:
diff --git a/oncopipe/oncopipe/__init__.py b/oncopipe/oncopipe/__init__.py
index 3a2b31ef..f4afd253 100755
--- a/oncopipe/oncopipe/__init__.py
+++ b/oncopipe/oncopipe/__init__.py
@@ -9,6 +9,7 @@
 import collections.abc
 from datetime import datetime
 from collections import defaultdict, namedtuple
+from .__version__ import __version__
 
 import yaml
 import pandas as pd
@@ -1800,3 +1801,56 @@ def cleanup_module(module_config):
     # Add back the TSV fields
     for field in tsv_fields.keys():
         module_config[field] = tsv_fields[field]
+
+
+# Kostia functions
+def get_capture_space(module_config, sample_id, genome_build, seq_type, return_ext):
+    """Returns path to the file with capspace to be used for  genome build.
+
+    Parameters
+    ----------
+    module_config : dict
+        The module-specific configuration.
+    sample_id : str
+        The id for a specific sample for which capture space should be returned.
+        Allows for both normal and tumour id.
+    genome_build : str
+        The specific genome build for which to return capture space.
+        Allows to unambiguously handle samples aligned to different genome versions.
+    seq_type : str
+        The soecific seq type for which to return capture space.
+    return_ext : str
+        The extension of the capture space file to be returned (.bed, .vcf, .vcf.gz).
+
+    Returns
+    -------
+    str
+        The path to a file relative to the reference files parental directory.
+    """
+
+    # Convenient variable to access sample table
+    module_samples = module_config["samples"]
+
+    this_sample = module_samples.loc[(module_samples['sample_id'] == sample_id) &
+            (module_samples['genome_build'] == genome_build) &
+            (module_samples['seq_type'] == seq_type)]
+
+    if len(this_sample) != 1:
+        raise AssertionError("Found %s matches when examining the sample table for pair \'%s\' \'%s\' \'%s\'" % (len(sample), sample_id, genome_build, seq_type))
+
+    if "capture_space" in this_sample.columns:
+        panel = this_sample.iloc[0]['capture_space']
+    else:
+        panel = "none"
+
+    # If this panel is "none" (aka not specified) use the default for this reference genome
+    if panel.upper() in (name.upper() for name in ['none', "na", "n/a", ""]):
+        try:
+            if "38" in genome_build:
+                panel = "exome-utr-grch38"
+            else:
+                panel = "exome-utr-grch37"
+        except KeyError as e:
+            raise AttributeError("No default capture space was specified for genome version \'%s\'. You can specify a default by setting \'default=\'true\'\' in a \'%s\'-based capture space in the reference config" % (genome_version, genome_version)) from e
+    # Now that we have found the corresponding capture region for this sample, obtain the requested file
+    return "genomes/" + genome_build + "/capture_space/" + panel + ".padded." + return_ext
diff --git a/oncopipe/oncopipe/__version__.py b/oncopipe/oncopipe/__version__.py
index a5673be8..8c861b0f 100644
--- a/oncopipe/oncopipe/__version__.py
+++ b/oncopipe/oncopipe/__version__.py
@@ -6,7 +6,7 @@
 
 __title__ = "oncopipe"
 __description__ = "Functions for running Snakemake modules"
-__version__ = "1.0.11"
+__version__ = "1.0.12"
 __author__ = "Bruno Grande"
 __author_email__ = "bgrande@sfu.ca"
 __license__ = "MIT"
diff --git a/workflows/reference_files/2.4/config/default.yaml b/workflows/reference_files/2.4/config/default.yaml
index 9c4d0a02..1ad75c50 100644
--- a/workflows/reference_files/2.4/config/default.yaml
+++ b/workflows/reference_files/2.4/config/default.yaml
@@ -47,6 +47,42 @@ genome_builds:
         version: "grch38"
         provider: "ucsc"
         genome_fasta_url: "https://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.fa.masked.gz"
+    hg19-reddy:
+        # Version of hg19 with chrM at the start, and chrM with a length of 16569bp. Used for the Reddy dataset
+        version: "grch37"
+        provider: "ucsc"
+        genome_fasta_url: "https://www.bcgsc.ca/downloads/lcr-modules/genome_fastas/hg19-reddy.fa"
+    hg38-nci:
+        # NCI's version of GRCh38, with a costco-sized flat pack of decoys
+        version: "grch38"
+        provider: "ucsc"
+        genome_fasta_url: "https://www.bcgsc.ca/downloads/lcr-modules/genome_fastas/grch38-nci.fa"
+    hg38-panea:
+        # Version of hg38 used by Panea et al.
+        version: "grch38"
+        provider: "ucsc"
+        genome_fasta_url: "https://www.bcgsc.ca/downloads/lcr-modules/genome_fastas/hg38-panea.fa"
+
+capture_space:
+    exome-utr-grch38:
+        genome: "grch38"
+        provider: "ucsc"
+        default: "true"
+        capture_bed_url: "https://www.bcgsc.ca/downloads/lcr-modules/genome_fastas/capture_bed/grch38_all_genes.canonical.sort.bed4"
+    exome-utr-grch37:
+        genome: "grch37"
+        provider: "ensembl"
+        default: "true"
+        capture_bed_url: "https://www.bcgsc.ca/downloads/lcr-modules/genome_fastas/capture_bed/grch37_all_genes.canonical.sort.bed4"
+    # to add custom capture space, follow this example and fill in dictionary keys
+    #name_of_capture_panel:
+        #genome: "grch37" or "hg38" as example
+        #provider: "ensembl" or "ucsc"
+        #capture_bed_url: here provide a link enclosed in "" to download bed file for capture panel if it is available in internet
+        #capture_bed_file: this key is optional and in "" you can specify path to a local bed file with capture panel
+
+capture_params:
+    padding_size: "200"
 
 wildcard_values:
     gencode_release: ["33"]
@@ -57,6 +93,9 @@ wildcard_values:
     rm_version: ["hg19", "hg38"]
 
 tools:
+    bedtools:
+        conda_env: "envs/bedtools-2.29.2.yaml"
+        version: "2.29.2"
     coreutils: 
         conda_env: "envs/coreutils-8.31.yaml"
         version: "8.31"
@@ -66,6 +105,9 @@ tools:
     samtools: 
         conda_env: "envs/samtools-1.9.yaml"
         version: "1.9"
+    tabix:
+        conda_env: "envs/tabix-0.2.6.yaml"
+        version: "0.2.6"
     bwa: 
         conda_env: "envs/bwa-0.7.17.yaml"
         version: "0.7.17"
diff --git a/workflows/reference_files/2.4/envs/bedtools-2.29.2.yaml b/workflows/reference_files/2.4/envs/bedtools-2.29.2.yaml
new file mode 120000
index 00000000..c185b12a
--- /dev/null
+++ b/workflows/reference_files/2.4/envs/bedtools-2.29.2.yaml
@@ -0,0 +1 @@
+../../../../envs/bedtools/bedtools-2.29.2.yaml
\ No newline at end of file
diff --git a/workflows/reference_files/2.4/envs/tabix-0.2.6.yaml b/workflows/reference_files/2.4/envs/tabix-0.2.6.yaml
new file mode 120000
index 00000000..bcf351f2
--- /dev/null
+++ b/workflows/reference_files/2.4/envs/tabix-0.2.6.yaml
@@ -0,0 +1 @@
+../../../../envs/tabix/tabix-0.2.6.yaml
\ No newline at end of file
diff --git a/workflows/reference_files/2.4/reference_files.smk b/workflows/reference_files/2.4/reference_files.smk
index 59d22ba8..f3e3a831 100644
--- a/workflows/reference_files/2.4/reference_files.smk
+++ b/workflows/reference_files/2.4/reference_files.smk
@@ -101,7 +101,7 @@ rule get_sdf_refs:
     output: 
         sdf = directory("genomes/{genome_build}/sdf")
     wildcard_constraints: 
-        genome_build = "hg38|hg19|grch37|hs37d5"
+        genome_build = "|".join(SDF_GENOME_BUILDS)
     shell: 
         "ln -srfT {input.sdf} {output.sdf}"
 
@@ -429,6 +429,130 @@ rule get_mutect2_small_exac:
         """)
 
 
+### FOR HANDLING CAPTURE SPACE/TARGETED SEQUENCING DATA ###
+# Added by Chris
+# What this *should* do (if I have written these rules correctly) is obtain a capture space BED file
+# check the contig names against the reference (and replace them as necessary), pad, sort,merge, and generate a bgzip/tabix
+# indexed version of the BED as well as an interval list.
+
+def _check_capspace_provider(w):
+    # Checks to determine if both the capture space BED and associated reference genome
+    # are chr prefixed or not
+
+    # If this is specified as the "default", make sure we obtain the relevent capture space
+    default_key = "default-" + w.genome_build
+    if default_key not in config["capture_space"] and w.capture_space == default_key:
+        # aka if the user hasn't explicitly specified a default using a default name
+        capture_space = _get_default_capspace(w)
+    else:
+        capture_space = w.capture_space
+
+    genome_provider = config["genome_builds"][w.genome_build]["provider"]
+    bed_provider = config["capture_space"][capture_space]["provider"]
+    
+    # If the providers match (i.e. they share the same prefix), just use the downloaded version
+    if genome_provider == bed_provider:
+        return {'bed': expand(rules.download_capspace_bed.output.capture_bed, capture_space=capture_space, genome_build=w.genome_build)}
+    else:
+        # Prompt the prefix to be converted
+        chr_status = "chr" if genome_provider == "ucsc" else "no_chr"
+        return {'bed': expand(rules.add_remove_chr_prefix_bed.output.converted_bed, capture_space = capture_space, genome_build = w.genome_build, chr_status= chr_status)}
+
+
+rule get_capspace_bed_download:
+    input:
+        unpack(_check_capspace_provider)
+    output:
+        capture_bed = "genomes/{genome_build}/capture_space/{capture_space}.bed"
+    conda: CONDA_ENVS["coreutils"]
+    shell:
+        "ln -srf {input.bed} {output.capture_bed}"
+
+
+rule sort_and_pad_capspace:
+    input:
+       capture_bed = rules.get_capspace_bed_download.output.capture_bed,
+       fai = rules.index_genome_fasta.output.fai
+    output:
+        intermediate_bed = temp("genomes/{genome_build}/capture_space/{capture_space}.intermediate.bed"),
+        padded_bed = "genomes/{genome_build}/capture_space/{capture_space}.padded.bed"
+    params:
+        padding_size = config['capture_params']['padding_size']  # Default to 200. I would be warry of changing
+    log:
+        "genomes/{genome_build}/capture_space/{capture_space}.padded.bed.log"
+    conda: CONDA_ENVS["bedtools"]
+    shell:
+        op.as_one_line("""
+        cat {input.fai} | cut -f 1-2 | perl -ane 'print "$F[0]\\t0\\t$F[1]\\n"' | bedtools intersect -wa -a {input.capture_bed} -b stdin > {output.intermediate_bed}
+            &&
+        bedtools slop -b {params.padding_size} -i {output.intermediate_bed} -g {input.fai} | bedtools sort | bedtools merge > {output.padded_bed} 2> {log}
+        """)
+
+rule check_capspace_contigs:
+    input:
+        bed = rules.get_capspace_bed_download.output.capture_bed,
+        fai = rules.index_genome_fasta.output.fai
+    output:
+        contig_log = "genomes/{genome_build}/capture_space/{capture_space}.check_contigs.log"
+    run:
+        # Parse BED contigs
+        bed_contigs = set()
+        with open(input.bed) as f:
+            for line in f:
+                line = line.rstrip()
+                contig = line.split("\t")[0]
+                if contig not in bed_contigs:
+                    bed_contigs.add(contig)
+
+        # Parse fai contigs
+        fai_contigs = set()
+        with open(input.fai) as f:
+            for line in f:
+                line = line.rstrip()
+                contig = line.split('\t')[0]
+                if contig not in fai_contigs:
+                    fai_contigs.add(contig)
+
+        # Check the BED file for contigs that are not in the reference genome
+        missing_contigs = list(x for x in bed_contigs if x not in fai_contigs)
+        with open(output.contig_log, "w") as o:
+            if len(missing_contigs) == 0:
+                o.write("No contigs missing from reference")
+            else:
+                o.write("The following contigs were missing from the reference\n")
+                o.write("\n".join(missing_contigs))
+            o.write("\n")
+
+
+rule compress_index_capspace_bed:
+    input:
+        capture_bed = rules.sort_and_pad_capspace.output.padded_bed
+    output:
+        bgzip_bed = "genomes/{genome_build}/capture_space/{capture_space}.padded.bed.gz",
+        tabix = "genomes/{genome_build}/capture_space/{capture_space}.padded.bed.gz.tbi"
+    log:
+        "genomes/{genome_build}/capture_space/{capture_space}.padded.bed.gz.log"
+    conda: CONDA_ENVS["tabix"]
+    shell:
+        op.as_one_line("""
+        bgzip -c {input.capture_bed} > {output.bgzip_bed}
+            &&
+        tabix -p bed {output.bgzip_bed}
+        """)
+
+
+rule create_interval_list:
+    input:
+        bed = rules.sort_and_pad_capspace.output.padded_bed,
+        sd = rules.create_gatk_dict.output.dict
+    output:
+        interval_list = "genomes/{genome_build}/capture_space/{capture_space}.padded.interval_list"
+    log:
+        "genomes/{genome_build}/capture_space/{capture_space}.padded.interval_list.log"
+    conda: CONDA_ENVS["gatk"]
+    shell:
+        "gatk BedToIntervalList --INPUT {input.bed} -SD {input.sd} -O {output.interval_list} > {log} 2>&1"
+
 ##### SigProfiler #####
 
 rule download_sigprofiler_genome:
@@ -459,3 +583,4 @@ rule install_sigprofiler_genome:
     run:
         op.relative_symlink(input, output.complete)
 
+
diff --git a/workflows/reference_files/2.4/reference_files_header.smk b/workflows/reference_files/2.4/reference_files_header.smk
index c2f0514e..d2326396 100644
--- a/workflows/reference_files/2.4/reference_files_header.smk
+++ b/workflows/reference_files/2.4/reference_files_header.smk
@@ -44,6 +44,23 @@ VERSION_UPPER = {
     "grch38": "GRCh38",
 }
 
+GENOME_VERSION_GROUPS = {}
+GENOME_VERSION_MAP = {}
+for genome_build in VERSION_UPPER.keys():
+    GENOME_VERSION_GROUPS[genome_build] = []
+
+# For Starfish SDF files
+SDF_VERSION_MAP = {}
+SDF_GENOME_BUILDS = []
+SDF_IGNORE = {"grch38", "grch38-legacy", "grch38_masked"}  # Ignore non-chr prefixed versions of hg38 since we don't use them
+sdf_genome_mappings = {
+"GRCh37": {"ensembl": "1000g_v37_phase2.sdf", "ucsc": "hg19.sdf"},
+"GRCh38": {"ucsc": "GRCh38.sdf"}
+}
+
+
+DEFAULT_CAPSPACE = {}
+
 # Check genome build versions, providers, and genome_fasta
 possible_versions = list(VERSION_UPPER.keys())
 possible_providers = ["ensembl", "ucsc", "gencode", "ncbi"]
@@ -51,7 +68,11 @@ for build_name, build_info in config["genome_builds"].items():
     assert "version" in build_info and build_info["version"] in possible_versions, (
         f"`version` not set for `{build_name}` or `version` not among {possible_versions}."
     )
-    assert "provider" in build_info and build_info["provider"] in possible_providers, (
+    GENOME_VERSION_GROUPS[build_info["version"]].append(build_name)
+    upper_genome_name = VERSION_UPPER[build_info["version"]]
+    GENOME_VERSION_MAP[build_name] = upper_genome_name
+    genome_provider = build_info["provider"]
+    assert "provider" in build_info and genome_provider in possible_providers, (
         f"`provider` not set for `{build_name}` or `provider` not among {possible_providers}."
     )
     assert "genome_fasta_url" in build_info, f"`genome_fasta_url` not set for `{build_name}`."
@@ -60,6 +81,36 @@ for build_name, build_info in config["genome_builds"].items():
         f"Pinging `genome_fasta_url` for {build_name} returned HTTP code {url_code} "
         f"(rather than 200): \n{build_info['genome_fasta_url']}"
     )    
+    # Find the appropriate SDF file for this genome build
+    if build_name not in SDF_IGNORE:
+        SDF_GENOME_BUILDS.append(build_name)
+        try:
+            SDF_VERSION_MAP[build_name] = sdf_genome_mappings[upper_genome_name][genome_provider]
+        except KeyError as e:
+            raise AttributeError(f"Unable to locate a Starfish SDF file for genome build \'{upper_genome_name}\' and provider \'{genome_provider}\'") from e
+
+# Check parent genome, provider for the capture space
+for build_name, build_info in config["capture_space"].items():
+    assert "provider" in build_info and build_info["provider"] in possible_providers, (
+        f"`provider` not set for `{build_name}` or `provider` not among {possible_providers}."
+        )
+    assert "genome" in build_info and build_info["genome"] in possible_versions,(
+        f"`genome` not set for `{build_name}` or `genome` not among {possible_versions}." )
+    assert "capture_bed_url" in build_info
+    url_code = urllib.request.urlopen(build_info["capture_bed_url"]).getcode()
+    assert url_code == 200, (
+         f"Pinging `capture_bed_url` for {build_name} returned HTTP code {url_code} "
+         f"(rather than 200): \n{build_info['capture_bed_url']}"
+        )
+    if "default" in build_info:
+        assert build_info["default"].lower() in ["true", "false"], (
+            f"true/false required for for \'default\' field"
+            )
+        build_version = build_info["genome"]
+        if build_version in DEFAULT_CAPSPACE:
+            # i.e. a default has already been specified for this genome version!
+            raise AttributeError("For reference genome version \'%s\', both \'%s\' and \'%s\' were specified as default capture spaces in the reference config" % (build_version, DEFAULT_CAPSPACE[build_version], build_name))
+        DEFAULT_CAPSPACE[build_info["genome"]] = build_name
 
 
 ##### TOOLS #####
@@ -122,16 +173,22 @@ for chrom_map_file in CHROM_MAPPINGS_FILES:
 
 
 rule download_genome_fasta:
-    output: 
+    output:
         fasta = "downloads/genome_fasta/{genome_build}.fa"
-    log: 
+    log:
         "downloads/genome_fasta/{genome_build}.fa.log"
     wildcard_constraints:
         genome_build = ".+(?<!masked)"
-    params: 
-        url = lambda w: config["genome_builds"][w.genome_build]["genome_fasta_url"]
+    params:
+        path = lambda w: config["genome_builds"][w.genome_build]["genome_fasta_file"] if "genome_fasta_file" in config["genome_builds"][w.genome_build] else config["genome_builds"][w.genome_build]["genome_fasta_url"],
     shell:
-        "curl -L {params.url} > {output.fasta} 2> {log}"
+        op.as_one_line("""
+        if [ -e {params.path} ]; then
+            cat {params.path} > {output.fasta} 2> {log};
+        else
+            curl -L {params.path} > {output.fasta} 2> {log};
+        fi
+        """)
 
 rule download_masked_genome_fasta:
     output:
@@ -345,13 +402,8 @@ rule download_liftover_chains:
 rule download_sdf: 
     output: 
         sdf = directory("downloads/sdf/{genome_build}/sdf")
-    params: 
-        build = lambda w: {
-            "grch37": "1000g_v37_phase2.sdf", 
-            "hs37d5": "1000g_v37_phase2.sdf",
-            "hg19": "hg19.sdf", 
-            "hg38": "GRCh38.sdf"
-        }[w.genome_build]
+    params:
+        build = lambda w: SDF_VERSION_MAP[w.genome_build]
     shell: 
         op.as_one_line("""
         wget -qO {output.sdf}.zip https://s3.amazonaws.com/rtg-datasets/references/{params.build}.zip && 
@@ -377,10 +429,11 @@ def get_matching_download_rules(file):
         # At least one output file should produce
         num_matches = []
         for output_file in r.output:
-            assert "{version}" in output_file, (
-                f"The `{rule_name}` download rule doesn't have a `{{version}}` "
-                f"wildcard in the output file ('{output_file}')."
-            )
+            if rule_name != "download_capspace_bed":  # Workaround since we don't really care about the provider for the capture space
+                assert "{version}" in output_file, (
+                    f"The `{rule_name}` download rule doesn't have a `{{version}}` "
+                    f"wildcard in the output file ('{output_file}')."
+                )
             matches = smk.io.glob_wildcards(output_file, [file])
             num_matches.append(len(matches[0]))
         if any(num > 0 for num in num_matches):
@@ -476,6 +529,57 @@ def get_download_file(file):
     return get_download_file_custom
 
 
+### CAPTURE SPACE ###
+rule download_capspace_bed:
+    output:
+        capture_bed = "downloads/capture_space/{capture_space}.{genome_build}.bed"
+    log:
+        "downloads/capture_space/{capture_space}.{genome_build}.bed.log"
+    params:
+        path = lambda w: config["capture_space"][w.capture_space]["capture_bed_file"] if "capture_bed_file" in config["capture_space"][w.capture_space] else config["capture_space"][w.capture_space]["capture_bed_url"],
+        provider = lambda w: config["capture_space"][w.capture_space]["provider"]
+    shell:
+        op.as_one_line("""
+        if [ -e {params.path} ]; then
+            cat {params.path} > {output.capture_bed} 2> {log};
+        else
+            curl -L {params.path} > {output.capture_bed} 2> {log};
+        fi
+        """)
+
+rule add_remove_chr_prefix_bed:
+    input:
+        capture_bed = rules.download_capspace_bed.output.capture_bed
+    output:
+        converted_bed = "downloads/capture_space/{capture_space}.{genome_build}.{chr_status}.bed"
+    run:
+        # Converts the specified BED file and adds/removes chr prefixes
+        if wildcards.chr_status == "chr":  # i.e. we need to add a chr prefix
+            add_chr = True
+        else:
+            add_chr = False
+
+        # Process the BED file
+        with open(input.capture_bed) as f, open(output.converted_bed, "w") as o:
+            i = 0
+            for line in f:
+                i += 1
+                # Make sure that this BED entry is chr-prefixed or not
+                if add_chr and line.startswith("chr"):
+                    # We were asked to add a chr prefix, but one already exists
+                    raise AttributeError("I was asked to add a \'chr\' prefix to \'%s\', but that BED is already \'chr\' prefixed on line %s" % (input.capture_bed, line))
+                if not add_chr and not line.startswith("chr"):
+                    # We were asked to remove a chr prefix, but there isn't one
+                    raise AttributeError("I was asked to remove a \'chr\' prefix \'%s\', but it isn't chr prefixed on line %s" % (input.capture_bed, line))
+
+                if add_chr:
+                    line = "chr" + line
+                else:
+                    line = line.replace("chr", "")
+
+                o.write(line)
+
+
 ##### SHARED #####