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diskin-lab-chop / AutoGVP

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Include variant depth in final output #176

Closed rjcorb closed 12 months ago

rjcorb commented 12 months ago

Purpose/implementation Section

What feature is being added or bug is being addressed?

Closes #175. This PR adds DP (from FORMAT field) to output_colnames.tsv so that it is included in full autogvp output.

What was your approach?

What GitHub issue does your pull request address?

175

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Please run on test files and ensure DP is included in output: 

bash run_autogvp.sh --workflow="cavatica" \
--vcf=input/test_pbta.single.vqsr.filtered.vep_105.vcf \
--filter_criteria='INFO/AF>=0.2 FORMAT/DP>=10 (gnomad_3_1_1_AF_non_cancer<0.001|gnomad_3_1_1_AF_non_cancer=".")' \
--intervar=input/test_pbta.hg38_multianno.txt.intervar \
--multianno=input/test_pbta.hg38_multianno.txt \
--autopvs1=input/test_pbta.autopvs1.tsv \
--outdir=../results \
--out="test_pbta"

Is there anything that you want to discuss further?

NOTE: these test files are now outdated since upstream updates to autopvs1, so please just confirm presence of DP column in output.

Documentation Checklist

naqvia commented 12 months ago

I see the DP field in the output_colnames.tsv but I do not see it in the final output. I see the following header names:

sample_id chr start ref alt rs_id gene_symbol_vep variant_classification_vep HGVSg HGVSc HGVSp autogvp_call autogvp_call_reason clinvar_stars clinvar_clinsig_autogvp clinvar_review_status_autogvp intervar_evidence criterion_autopvs1 PVS1_autogvp BA1_autogvp PS_autogvp PM_autogvp PP_autogvp BS_autogvp BP_autogvp intervar_adjusted clinvar_variant_id clinvar_date_last_evaluated variant_impact_vep ensembl_gene_vep ensembl_transcript_vep biotype_vep exon_vep intron_vep cDNA_position_vep cds_position_vep protein_position_vep amino_acids_vep codons_vep distance_vep strand_vep pick_vep gene_symbol_source_vep hgnc_id_vep canonical_vep csq_vep clinvar_variant_link