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feat(HiPhase): Phase TRGT VCF with HiPhase #107

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feat(HiPhase): Phase TRGT VCF with HiPhase #107

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7aac070
feat(HiPhase): Phase TRGT VCF with HiPhase
williamrowell Jan 10, 2024
2ea1376
Updated submodule to increase memory for HiPhase, DeepVariant, and PBSV
williamrowell Jan 17, 2024
0297431
Merge branch 'develop' into feature/hiphase-1.1
williamrowell Feb 16, 2024
4a092a2
update wdl-ci config file after successful tests
github-actions[bot] Feb 16, 2024
ed911d8
Merge branch 'develop' into feature/hiphase-1.1
williamrowell Feb 16, 2024
b3ae1f1
Fix TRGT version number in docs
williamrowell Feb 16, 2024
6e8ebe0
fix(pbsv): Set mem for pbsv_discover to 10GB.
williamrowell Feb 17, 2024
21fac20
update wdl-ci config file after successful tests
github-actions[bot] Feb 17, 2024
c69da58
fix(deepvariant): Decompress custom deepvariant models to writable lo…
williamrowell Feb 17, 2024
74a7df1
Merge remote-tracking branch 'refs/remotes/origin/feature/hiphase-1.1…
williamrowell Feb 17, 2024
6a1ec7e
update wdl-ci config file after successful tests
github-actions[bot] Feb 17, 2024
4afd6c9
Merge branch 'develop' into feature/hiphase-1.1
williamrowell Mar 9, 2024
b8b81b7
feat(trgt): Normalize TRGT output names by providing explicit sample.…
williamrowell Mar 9, 2024
54a0b2b
feat(hiphase): Normalize HiPhase BAM outputs if only one BAM is to be…
williamrowell Mar 9, 2024
9c6b203
Merge remote-tracking branch 'refs/remotes/origin/feature/hiphase-1.1…
williamrowell Mar 9, 2024
3898bf4
fix(glnexus): Clean up large intermediate files from glnexus.
williamrowell Mar 9, 2024
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8 changes: 4 additions & 4 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -205,8 +205,8 @@ These files will be output for each sample defined in the cohort.
| Array[File] | sample_hiphase_blocks | Phase block list written by [HiPhase](https://github.com/PacificBiosciences/HiPhase/blob/main/docs/user_guide.md#phase-block-file---blocks-file) | |
| Array[File] | sample_hiphase_haplotags | Per-read haplotag information, written by [HiPhase](https://github.com/PacificBiosciences/HiPhase/blob/main/docs/user_guide.md#haplotag-file---haplotag-file) | |
| Array[[IndexData](https://github.com/PacificBiosciences/wdl-common/blob/main/wdl/structs.wdl)] | merged_haplotagged_bam | Aligned (by [pbmm2](https://github.com/PacificBiosciences/pbmm2)), haplotagged (by [HiPhase](https://github.com/PacificBiosciences/HiPhase/blob/main/docs/user_guide.md#haplotagged-bam-files)) reads (with index) | |
| Array[File] | haplotagged_bam_mosdepth_summary | [mosdepth](https://github.com/brentp/mosdepth) summary of median depths per chromosome | |
| Array[File] | haplotagged_bam_mosdepth_region_bed | mosdepthhttps://github.com/brentp/mosdepth BED of median coverage depth per 500 bp window | |
| Array[File] | mosdepth_summary | [mosdepth](https://github.com/brentp/mosdepth) summary of median depths per chromosome | |
| Array[File] | mosdepth_region_bed | mosdepth BED of median coverage depth per 500 bp window | |
| Array[[IndexData](https://github.com/PacificBiosciences/wdl-common/blob/main/wdl/structs.wdl)] | trgt_repeat_vcf | Tandem repeat genotypes from [TRGT](https://github.com/PacificBiosciences/trgt/blob/main/docs/vcf_files.md) (with index) | |
| Array[[IndexData](https://github.com/PacificBiosciences/wdl-common/blob/main/wdl/structs.wdl)] | trgt_spanning_reads | Fragments of HiFi reads spanning loci genotyped by TRGT (with index) | |
| Array[File] | trgt_dropouts | Regions with insufficient coverage to genotype by TRGT | |
Expand Down Expand Up @@ -259,7 +259,7 @@ The Docker image used by a particular step of the workflow can be identified by
| deepvariant | User-defined; default is version [1.6.0](https://github.com/google/deepvariant/releases/tag/v1.6.0) | [DeepVariant GitHub](https://github.com/google/deepvariant) |
| glnexus | <ul><li>[glnexus v1.4.3](https://github.com/dnanexus-rnd/GLnexus/releases/tag/v1.4.3)</li></ul> | [GLnexus GitHub](https://github.com/dnanexus-rnd/GLnexus) |
| hificnv | <ul><li>[HiFiCNV v0.1.7](https://github.com/PacificBiosciences/HiFiCNV/releases/tag/v0.1.7)</li><li>[bcftools 1.16](https://github.com/samtools/bcftools/releases/tag/1.16)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/0b0fbe939648087e9fdea4497ae08dc76538ebf0/docker/hificnv) |
| hiphase | <ul><li>[HiPhase 1.0.0](https://github.com/PacificBiosciences/HiPhase/releases/tag/v1.0.0)</li><li>[samtools 1.18](https://github.com/samtools/samtools/releases/tag/1.18)</li><li>[bcftools 1.18](https://github.com/samtools/bcftools/releases/tag/1.18)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/d26db6204409dfeff56e169cdba0cc14bc272f15/docker/hiphase) |
| hiphase | <ul><li>[HiPhase 1.1.0](https://github.com/PacificBiosciences/HiPhase/releases/tag/v1.1.0)</li><li>[samtools 1.18](https://github.com/samtools/samtools/releases/tag/1.18)</li><li>[bcftools 1.18](https://github.com/samtools/bcftools/releases/tag/1.18)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/02f2bae9d10504c587990995fba3aa7335f910f8/docker/hiphase) |
| htslib | <ul><li>[htslib 1.14](https://github.com/samtools/htslib/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/htslib) |
| mosdepth | <ul><li>[mosdepth 0.2.9](https://github.com/brentp/mosdepth/releases/tag/v0.2.9)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/mosdepth) |
| paraphase | <ul><li>[minimap2 2.26](https://github.com/lh3/minimap2/releases/tag/v2.26)</li><li>[samtools 1.18](https://github.com/samtools/samtools/releases/tag/1.18)</li><li>[paraphase 3.0.0](https://github.com/PacificBiosciences/paraphase)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/4f510e5f434cc138577853f56558b90e059fd770/docker/paraphase) |
Expand All @@ -270,7 +270,7 @@ The Docker image used by a particular step of the workflow can be identified by
| samtools | <ul><li>[samtools 1.14](https://github.com/samtools/samtools/releases/tag/1.14)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/samtools) |
| slivar | <ul><li>[slivar 0.2.2](https://github.com/brentp/slivar/releases/tag/v0.2.2)</li><li>[bcftools 1.14](https://github.com/samtools/bcftools/releases/tag/1.14)</li><li>[vcfpy 0.13.3](https://github.com/bihealth/vcfpy/releases/tag/v0.13.3)</li><li>[pysam 0.19.1](https://github.com/pysam-developers/pysam/releases/tag/v0.19.1)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3560fcc5a84e044067cea9c9a7669cfc2659178e/docker/slivar) |
| svpack | <ul><li>[svpack 36180ae6](https://github.com/PacificBiosciences/svpack/tree/a82598ebc4013bf32e70295b83b380ada6302c4a)</li><li>[htslib 1.18](https://github.com/samtools/htslib/releases/tag/1.18)</li><li>[pysam 0.21.0](https://github.com/pysam-developers/pysam/releases/tag/v0.21.0)</li> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/8edbc516abc0ff43ac279b48018003923721b054/docker/svpack) |
| trgt | <ul><li>[trgt 0.8.0](https://github.com/PacificBiosciences/trgt/releases/tag/v0.7.0)</li><li>[samtools 1.18](https://github.com/samtools/samtools/releases/tag/1.18)</li><li>[bcftools 1.18](https://github.com/samtools/bcftools/releases/tag/1.18)</li><li>[pysam 0.21.0](https://github.com/pysam-developers/pysam/releases/tag/v0.21.0)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3bbc033f8f942b10a304b4fa907957a789c73ef7/docker/trgt) |
| trgt | <ul><li>[trgt 0.8.0](https://github.com/PacificBiosciences/trgt/releases/tag/v0.8.0)</li><li>[samtools 1.18](https://github.com/samtools/samtools/releases/tag/1.18)</li><li>[bcftools 1.18](https://github.com/samtools/bcftools/releases/tag/1.18)</li><li>[pysam 0.21.0](https://github.com/pysam-developers/pysam/releases/tag/v0.21.0)</li></ul> | [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/3bbc033f8f942b10a304b4fa907957a789c73ef7/docker/trgt) |

---

Expand Down
6 changes: 3 additions & 3 deletions wdl-ci.config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -348,7 +348,7 @@
"tasks": {
"pbsv_discover": {
"key": "pbsv_discover",
"digest": "lbv7nwockw3wcbkfvapzoc2wv7fcodnw",
"digest": "winvogvhhjzlbxhsknadxpvwfj6f37wm",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -654,7 +654,7 @@
},
"deepvariant_postprocess_variants": {
"key": "deepvariant_postprocess_variants",
"digest": "ey7zqpajaeesvsg372rehhjmkpqld2qx",
"digest": "nxh4wiylfi7ngy6cxe65ovrzrwdoutja",
"tests": [
{
"inputs": {
Expand Down Expand Up @@ -881,7 +881,7 @@
"tasks": {
"run_hiphase": {
"key": "run_hiphase",
"digest": "6k2rtel3k6747xhcfnjufqfzgcnb7g5v",
"digest": "6qxqz7p56asf3z6f6cqwebdsd57fs4lh",
"tests": [
{
"inputs": {
Expand Down
4 changes: 2 additions & 2 deletions workflows/main.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -115,8 +115,8 @@ workflow humanwgs {
Array[File] sample_hiphase_blocks = sample_analysis.hiphase_blocks
Array[File] sample_hiphase_haplotags = sample_analysis.hiphase_haplotags
Array[IndexData] merged_haplotagged_bam = sample_analysis.merged_haplotagged_bam
Array[File] haplotagged_bam_mosdepth_summary = sample_analysis.haplotagged_bam_mosdepth_summary
Array[File] haplotagged_bam_mosdepth_region_bed = sample_analysis.haplotagged_bam_mosdepth_region_bed
Array[File] mosdepth_summary = sample_analysis.mosdepth_summary
Array[File] mosdepth_region_bed = sample_analysis.mosdepth_region_bed

# per sample trgt outputs
Array[IndexData] trgt_spanning_reads = sample_analysis.trgt_spanning_reads
Expand Down
166 changes: 88 additions & 78 deletions workflows/sample_analysis/sample_analysis.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -49,27 +49,8 @@ workflow sample_analysis {
}
}

call DeepVariant.deepvariant {
input:
sample_id = sample.sample_id,
aligned_bams = aligned_bam,
reference_fasta = reference.fasta,
reference_name = reference.name,
deepvariant_version = deepvariant_version,
custom_deepvariant_model_tar = custom_deepvariant_model_tar,
default_runtime_attributes = default_runtime_attributes
}

call bcftools {
input:
vcf = deepvariant.vcf.data,
stats_params = "--apply-filters PASS --samples ~{sample.sample_id}",
reference = reference.fasta.data,
runtime_attributes = default_runtime_attributes
}

scatter (shard_index in range(length(pbsv_splits))) {
Array[String] region_set = pbsv_splits[shard_index]
Array[String] region_set = pbsv_splits[shard_index]

call PbsvCall.pbsv_call {
input:
Expand All @@ -84,6 +65,7 @@ workflow sample_analysis {
}
}

# concatenate pbsv vcfs
call ConcatVcf.concat_vcf {
input:
vcfs = pbsv_call.pbsv_vcf,
Expand All @@ -92,73 +74,97 @@ workflow sample_analysis {
runtime_attributes = default_runtime_attributes
}

IndexData zipped_pbsv_vcf = {
"data": concat_vcf.concatenated_vcf,
"data_index": concat_vcf.concatenated_vcf_index
}

call HiPhase.hiphase {
# vcfs order: small variants, SVs
input:
id = sample.sample_id,
refname = reference.name,
sample_ids = [sample.sample_id],
vcfs = [deepvariant.vcf, zipped_pbsv_vcf],
bams = aligned_bam,
haplotag = true,
reference_fasta = reference.fasta,
default_runtime_attributes = default_runtime_attributes
}

# merge haplotagged bams if there are multiple
if (length(hiphase.haplotagged_bams) > 1) {
scatter (bam_object in hiphase.haplotagged_bams) {
# merge aligned bams if there are multiple
if (length(aligned_bam) > 1) {
scatter (bam_object in aligned_bam) {
File bam_to_merge = bam_object.data
}
call merge_bams {
input:
bams = bam_to_merge,
output_bam_name = "~{sample.sample_id}.~{reference.name}.haplotagged.bam",
output_bam_name = "~{sample.sample_id}.~{reference.name}.bam",
runtime_attributes = default_runtime_attributes
}
}

# select the merged bam if it exists, otherwise select the first (only) haplotagged bam
File haplotagged_bam = select_first([merge_bams.merged_bam, hiphase.haplotagged_bams[0].data])
File haplotagged_bam_index = select_first([merge_bams.merged_bam_index, hiphase.haplotagged_bams[0].data_index])
# select the merged bam if it exists, otherwise select the first (only) aligned bam
File aligned_bam_data = select_first([merge_bams.merged_bam, aligned_bam[0].data])
File aligned_bam_index = select_first([merge_bams.merged_bam_index, aligned_bam[0].data_index])

call Mosdepth.mosdepth {
input:
aligned_bam = haplotagged_bam,
aligned_bam_index = haplotagged_bam_index,
aligned_bam = aligned_bam_data,
aligned_bam_index = aligned_bam_index,
runtime_attributes = default_runtime_attributes
}

call DeepVariant.deepvariant {
input:
sample_id = sample.sample_id,
aligned_bams = aligned_bam,
reference_fasta = reference.fasta,
reference_name = reference.name,
deepvariant_version = deepvariant_version,
custom_deepvariant_model_tar = custom_deepvariant_model_tar,
default_runtime_attributes = default_runtime_attributes
}

call bcftools {
input:
vcf = deepvariant.vcf.data,
stats_params = "--apply-filters PASS --samples ~{sample.sample_id}",
reference = reference.fasta.data,
runtime_attributes = default_runtime_attributes
}

call trgt {
input:
sample_id = sample.sample_id,
sex = sample.sex,
bam = haplotagged_bam,
bam_index = haplotagged_bam_index,
bam = aligned_bam_data,
bam_index = aligned_bam_index,
reference = reference.fasta.data,
reference_index = reference.fasta.data_index,
tandem_repeat_bed = reference.trgt_tandem_repeat_bed,
output_prefix = "~{sample.sample_id}.~{reference.name}",
runtime_attributes = default_runtime_attributes
}

call HiPhase.hiphase {
# vcfs order: small variants, SVs, TRGT
input:
id = sample.sample_id,
refname = reference.name,
sample_ids = [sample.sample_id],
vcfs = [
deepvariant.vcf,
{"data": concat_vcf.concatenated_vcf, "data_index": concat_vcf.concatenated_vcf_index},
{"data": trgt.repeat_vcf, "data_index": trgt.repeat_vcf_index}
],
bams = [{"data": aligned_bam_data, "data_index": aligned_bam_index}],
haplotag = true,
reference_fasta = reference.fasta,
default_runtime_attributes = default_runtime_attributes
}

IndexData haplotagged_bam = {
"data": hiphase.haplotagged_bams[0].data,
"data_index": hiphase.haplotagged_bams[0].data_index
}

call coverage_dropouts {
input:
bam = haplotagged_bam,
bam_index = haplotagged_bam_index,
bam = haplotagged_bam.data,
bam_index = haplotagged_bam.data_index,
tandem_repeat_bed = reference.trgt_tandem_repeat_bed,
output_prefix = "~{sample.sample_id}.~{reference.name}",
runtime_attributes = default_runtime_attributes
}

call cpg_pileup {
input:
bam = haplotagged_bam,
bam_index = haplotagged_bam_index,
bam = haplotagged_bam.data,
bam_index = haplotagged_bam.data_index,
output_prefix = "~{sample.sample_id}.~{reference.name}",
reference = reference.fasta.data,
reference_index = reference.fasta.data_index,
Expand All @@ -168,8 +174,8 @@ workflow sample_analysis {
call paraphase {
input:
sample_id = sample.sample_id,
bam = haplotagged_bam,
bam_index = haplotagged_bam_index,
bam = haplotagged_bam.data,
bam_index = haplotagged_bam.data_index,
reference = reference.fasta.data,
reference_index = reference.fasta.data_index,
out_directory = "~{sample.sample_id}.paraphase",
Expand All @@ -180,8 +186,8 @@ workflow sample_analysis {
input:
sample_id = sample.sample_id,
sex = sample.sex,
bam = haplotagged_bam,
bam_index = haplotagged_bam_index,
bam = haplotagged_bam.data,
bam_index = haplotagged_bam.data_index,
phased_vcf = hiphase.phased_vcfs[0].data,
phased_vcf_index = hiphase.phased_vcfs[0].data_index,
reference = reference.fasta.data,
Expand All @@ -195,33 +201,36 @@ workflow sample_analysis {
}

output {
# per movie stats, alignments, and svsigs
# per movie stats, alignments
Array[File] bam_stats = pbmm2_align.bam_stats
Array[File] read_length_summary = pbmm2_align.read_length_summary
Array[File] read_quality_summary = pbmm2_align.read_quality_summary
Array[IndexData] aligned_bams = aligned_bam

# phased_vcfs ouput order from HiPhase: small variants, SVs, TRGT

# per sample structural variant signatures and calls
IndexData phased_sv_vcf = hiphase.phased_vcfs[1]
Array[File] svsigs = pbsv_discover.svsig

# per sample small variant calls
IndexData phased_small_variant_vcf = hiphase.phased_vcfs[0]
IndexData small_variant_gvcf = deepvariant.gvcf
File small_variant_vcf_stats = bcftools.stats
File small_variant_roh_out = bcftools.roh_out
File small_variant_roh_bed = bcftools.roh_bed

# per sample final phased variant calls and haplotagged alignments
# phased_vcfs order: small variants, SVs
IndexData phased_small_variant_vcf = hiphase.phased_vcfs[0]
IndexData phased_sv_vcf = hiphase.phased_vcfs[1]
# per sample phasing stats and haplotagged alignments
File hiphase_stats = hiphase.hiphase_stats
File hiphase_blocks = hiphase.hiphase_blocks
File hiphase_haplotags = select_first([hiphase.hiphase_haplotags])
IndexData merged_haplotagged_bam = {"data": haplotagged_bam, "data_index": haplotagged_bam_index}
File haplotagged_bam_mosdepth_summary = mosdepth.summary
File haplotagged_bam_mosdepth_region_bed = mosdepth.region_bed
IndexData merged_haplotagged_bam = haplotagged_bam
File mosdepth_summary = mosdepth.summary
File mosdepth_region_bed = mosdepth.region_bed

# per sample trgt outputs
IndexData trgt_repeat_vcf = hiphase.phased_vcfs[2]
IndexData trgt_spanning_reads = {"data": trgt.spanning_reads, "data_index": trgt.spanning_reads_index}
IndexData trgt_repeat_vcf = {"data": trgt.repeat_vcf, "data_index": trgt.repeat_vcf_index}
File trgt_dropouts = coverage_dropouts.trgt_dropouts

# per sample cpg outputs
Expand Down Expand Up @@ -446,12 +455,13 @@ task trgt {
File reference_index
File tandem_repeat_bed

String output_prefix

RuntimeAttributes runtime_attributes
}

Boolean sex_defined = defined(sex)
String karyotype = if select_first([sex, "FEMALE"]) == "MALE" then "XY" else "XX"
String bam_basename = basename(bam, ".bam")
Int threads = 4
Int disk_size = ceil((size(bam, "GB") + size(reference, "GB")) * 2 + 20)

Expand All @@ -468,37 +478,37 @@ task trgt {
--genome ~{reference} \
--repeats ~{tandem_repeat_bed} \
--reads ~{bam} \
--output-prefix ~{bam_basename}.trgt
--output-prefix ~{output_prefix}.trgt

bcftools --version

bcftools sort \
--output-type z \
--output ~{bam_basename}.trgt.sorted.vcf.gz \
~{bam_basename}.trgt.vcf.gz
--output ~{output_prefix}.trgt.sorted.vcf.gz \
~{output_prefix}.trgt.vcf.gz

bcftools index \
--threads ~{threads - 1} \
--tbi \
~{bam_basename}.trgt.sorted.vcf.gz
~{output_prefix}.trgt.sorted.vcf.gz

samtools --version

samtools sort \
-@ ~{threads - 1} \
-o ~{bam_basename}.trgt.spanning.sorted.bam \
~{bam_basename}.trgt.spanning.bam
-o ~{output_prefix}.trgt.spanning.sorted.bam \
~{output_prefix}.trgt.spanning.bam

samtools index \
-@ ~{threads - 1} \
~{bam_basename}.trgt.spanning.sorted.bam
~{output_prefix}.trgt.spanning.sorted.bam
>>>

output {
File spanning_reads = "~{bam_basename}.trgt.spanning.sorted.bam"
File spanning_reads_index = "~{bam_basename}.trgt.spanning.sorted.bam.bai"
File repeat_vcf = "~{bam_basename}.trgt.sorted.vcf.gz"
File repeat_vcf_index = "~{bam_basename}.trgt.sorted.vcf.gz.tbi"
File spanning_reads = "~{output_prefix}.trgt.spanning.sorted.bam"
File spanning_reads_index = "~{output_prefix}.trgt.spanning.sorted.bam.bai"
File repeat_vcf = "~{output_prefix}.trgt.sorted.vcf.gz"
File repeat_vcf_index = "~{output_prefix}.trgt.sorted.vcf.gz.tbi"
}

runtime {
Expand Down
2 changes: 1 addition & 1 deletion workflows/wdl-common
Open in desktop
Submodule wdl-common updated 4 files
+3 −0 wdl/tasks/glnexus.wdl
+1 −1 wdl/tasks/pbsv_discover.wdl
+1 −1 wdl/workflows/deepvariant/deepvariant.wdl
+11 −5 wdl/workflows/hiphase/hiphase.wdl
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