GL-548 - Update CreateVat code to handle samples that do not contain all population groups. #7965
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…m the input ancestry file. Have GvsCreateVAT.wdl only pull fields from the VCF for the selected subpopulations. Update create_variant_annotation_table.py to set empty population-specific AC/AN/AF, etc. values if population is not present.
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CreateVAT workflow run on a quickstart with only two populations for the ten samples (amr, afr) here. |
Codecov Report
@@ Coverage Diff @@
## ah_var_store #7965 +/- ##
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Coverage ? 86.235%
Complexity ? 35200
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Files ? 2173
Lines ? 165016
Branches ? 17793
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Hits ? 142302
Misses ? 16385
Partials ? 6329 |
rsasch
suggested changes
Aug 1, 2022
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Sounds good - was thinking of doing that at the last moment (i.e. having the PR approved, build a 'ah_varstore_' docker off of this PR and then update the wdls and then merge. |
rsasch
approved these changes
Aug 1, 2022
RoriCremer
reviewed
Aug 1, 2022
| @@ -23,7 +23,6 @@ workflow GvsCreateVAT { | |||
| Array[String] contig_array = ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22", "chrX", "chrY", "chrM"] | |||
| File reference = "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta" | |||
| File nirvana_data_directory = "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/NirvanaData.tar.gz" | |||
| File AnAcAf_annotations_template = "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/vat/custom_annotations_template.tsv" | |||
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RoriCremer
approved these changes
Aug 1, 2022
This was referenced Mar 17, 2023
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Update GvsCreateVAT.wdl to build the subpopulation-specific files from the input ancestry file.
Have GvsCreateVAT.wdl only pull fields from the VCF for the selected subpopulations.
Update create_variant_annotation_table.py to set empty population-specific AC/AN/AF, etc. values if population is not present.