fix bug add todo

scholl-lab · Oct 19, 2023 · 4830a43 · 4830a43
1 parent 19b4782
commit 4830a43
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Showing 4 changed files with 17 additions and 5 deletions.
diff --git a/analyses/calling/README.md b/analyses/calling/README.md
@@ -58,4 +58,16 @@ The pipeline produces the following outputs in the output_folder specified in th
 - `variant_calls`: A folder containing the VCF files with the variant calls.
 - `logs`: A folder containing the log files for the MuTect2 runs.
 
-Each VCF file is named with the format `<individual1>_<analysis>_<chromosome>.vcf.gz`.
+Each VCF file is named with the format `<individual1>_<analysis>_<chromosome>.vcf.gz`.
+
+# TODO
+- [ ] script to merge VCF files, f1r2 files, and stats files
+    - use GatherVcfs (Picard) to merge VCF files
+    - use gatk MergeMutectStats to merge stats files
+    - the f1r2 files are not merged but are all used as input for LearnReadOrientationModel
+- [ ] script for LearnReadOrientationModel
+    - this should be part of the merge script
+- [ ] script for FilterMutectCalls
+- [ ] script for CalculateContamination (plus GetPileupSummaries)
+
+--> see: https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2
diff --git a/analyses/calling/bcftools_concat.smk b/analyses/calling/bcftools_concat.smk
@@ -78,7 +78,7 @@ SCATTER_NAME_PREFIX = config.get("scatter_name_prefix", "")
 # Define the scattering interval names based on the ranges and prefixes specified in the
 # configuration file. This allows for a flexible definition of intervals, accommodating 
 # various naming conventions and range specifications.
-SCATTERING_INTERVAL_RANGES = config.get("scattering_interval_ranges", [str(i) for i in range(1, 22)] + ['X', 'Y'])
+SCATTERING_INTERVAL_RANGES = config.get("scattering_interval_ranges", [str(i) for i in range(1, 23)] + ['X', 'Y'])
 SCATTERING_INTERVAL_NAMES = expand_interval_names(SCATTERING_INTERVAL_RANGES, SCATTER_NAME_PREFIX)
 
 # Get the delimiter for scatter names; default is "."

diff --git a/analyses/calling/merge_mutect2_calls.smk b/analyses/calling/merge_mutect2_calls.smk
@@ -37,7 +37,7 @@ MERGED_DIR = prefix_results('variant_merge')
 LOG_DIR = prefix_results('logs')
 
 # List of chromosomes for processing
-chromosomes = [f"chr{i}" for i in range(1, 22)] + ["chrX", "chrY"]
+chromosomes = [f"chr{i}" for i in range(1, 23)] + ["chrX", "chrY"]
 # ----------------------------------------------------------------------------------- #
 
 # ----------------------------------------------------------------------------------- #

diff --git a/analyses/calling/mutect2_calling.smk b/analyses/calling/mutect2_calling.smk
@@ -39,7 +39,7 @@ VARIANT_DIR = prefix_results('variant_calls')
 LOG_DIR = prefix_results('logs')
 
 # List of chromosomes to loop through
-chromosomes = [f"chr{i}" for i in range(1, 22)] + ["chrX", "chrY"]
+chromosomes = [f"chr{i}" for i in range(1, 23)] + ["chrX", "chrY"]
 # ----------------------------------------------------------------------------------- #
 
 # ----------------------------------------------------------------------------------- #
@@ -98,7 +98,7 @@ rule call_variants:
             $normal_sample_option \
             --germline-resource {params.af_only_gnomad} \
             --panel-of-normals {params.panel_of_normals} \
-            --f1r2-tar-gz {OUTPUT_DIR}/{params.individual}_{params.analysis}_{wildcards.chromosome}.f1r2.tar.gz \
+            --f1r2-tar-gz {VARIANT_DIR}/{params.individual}_{params.analysis}_{wildcards.chromosome}.f1r2.tar.gz \
             $scatter_option \
             -O {output.variant_file} 2> {log.mutect2}
         """