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317 remove excess header values in VCF extract #7786

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merged 5 commits into from
Apr 15, 2022
Merged

317 remove excess header values in VCF extract #7786

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3d4d04d
remove unwanted header
RoriCremer Apr 14, 2022
ffdac45
missed the extra NAY
RoriCremer Apr 14, 2022
da88e62
update dockstore
RoriCremer Apr 14, 2022
45e4187
use new headers jar
RoriCremer Apr 14, 2022
074c3bf
remove header lines from test too
RoriCremer Apr 15, 2022
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1 change: 1 addition & 0 deletions .dockstore.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -117,6 +117,7 @@ workflows:
branches:
- master
- ah_var_store
- rc-vs-317-remove-excess-headers
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Do we get rid of these before we merge the PR?

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Ideally yes, but with tests taking so long, sometimes we dont. It would be great to do a full clean up of all the extra branches in dockstore too

- name: GvsImportGenomes
subclass: WDL
primaryDescriptorPath: /scripts/variantstore/wdl/GvsImportGenomes.wdl
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsExtractCallset.wdl
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Expand Up @@ -15,7 +15,7 @@ workflow GvsExtractCallset {

File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list"
File interval_weights_bed = "gs://broad-public-datasets/gvs/weights/gvs_vet_weights_1kb.bed"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/rc-add-AD-04112022/gatk-package-4.2.0.0-498-g1f53709-SNAPSHOT-local.jar"
File gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/rc-update-headers-04142022/gatk-package-4.2.0.0-497-gda8a97a-SNAPSHOT-local.jar"
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Should these directory have the jira ticket number embedded (to see if the work has been merged into ah_var_store and so we can assume the directory and jar is stale / unneeded).

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@mcovarr mcovarr Apr 15, 2022 •
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Yeah I agree that would be good. With the combo of embedding the ticket number in the branch name and the "copy your custom GATK jar" script that Kristian shared the other day we seem to get that.

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I like this! Maybe post-Charlie we can consolidate a set of rules for jars? It's certainly too haphazard now


String output_file_base_name = filter_set_name

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6 changes: 1 addition & 5 deletions src/main/java/org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohort.java
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Expand Up @@ -211,17 +211,14 @@ protected static VCFHeader generateVcfHeader(Set<String> sampleNames,

// Filter fields
headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.LOW_QUAL_FILTER_NAME));
headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.NAY_FROM_YNG));
headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.EXCESS_HET_KEY));
headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.EXCESS_ALLELES));
headerLines.add(GATKVCFHeaderLines.getFilterLine(GATKVCFConstants.NO_HQ_GENOTYPES));

// Info fields
VCFStandardHeaderLines.addStandardInfoLines( headerLines, true,
VCFConstants.ALLELE_COUNT_KEY,
VCFConstants.ALLELE_FREQUENCY_KEY,
VCFConstants.ALLELE_NUMBER_KEY,
VCFConstants.END_KEY
VCFConstants.ALLELE_NUMBER_KEY
);
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_RAW_QUAL_APPROX_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.RAW_QUAL_APPROX_KEY));
Expand All @@ -231,7 +228,6 @@ protected static VCFHeader generateVcfHeader(Set<String> sampleNames,
VCFConstants.GENOTYPE_QUALITY_KEY
);
headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.REFERENCE_GENOTYPE_QUALITY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.EXCESS_HET_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_VQS_LOD_KEY));
headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.AS_YNG_STATUS_KEY));

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4 changes: 0 additions & 4 deletions ...org/broadinstitute/hellbender/tools/gvs/extract/ExtractCohort/ranges_extract.expected.vcf
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@@ -1,8 +1,6 @@
##fileformat=VCFv4.2
##FILTER=<ID=EXCESS_ALLELES,Description="Site has an excess of alternate alleles based on the input threshold (default is 6)">
##FILTER=<ID=ExcessHet,Description="Site has excess het value larger than the threshold">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=NAY,Description="Considered a NAY in the Yay, Nay, Grey table">
##FILTER=<ID=NO_HQ_GENOTYPES,Description="Site has no high quality variant genotypes">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
Expand All @@ -13,8 +11,6 @@
##INFO=<ID=AS_QUALapprox,Number=1,Type=String,Description="Allele-specific QUAL approximations">
##INFO=<ID=AS_VQSLOD,Number=A,Type=String,Description="For each alt allele, the log odds of being a true variant versus being false under the trained gaussian mixture model">
##INFO=<ID=AS_YNG,Number=A,Type=String,Description="For each alt allele, the yay/nay/grey status (yay are known good alleles, nay are known false positives, grey are unknown)">
##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">
##INFO=<ID=QUALapprox,Number=1,Type=Integer,Description="Sum of PL[0] values; used to approximate the QUAL score">
##contig=<ID=chr1,length=248956422,assembly=38>
##contig=<ID=chr2,length=242193529,assembly=38>
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