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diskin-lab-chop / AutoGVP

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Bug: First filtering criterion skipped #127

Closed rjcorb closed 1 year ago

rjcorb commented 1 year ago

Provide the command used or report the bug here

The first filtering criterion provided in the filtering_criteria argument is currently ignored. For example, when running the following command: 

bash run_autogvp.sh --workflow="cavatica" \
--vcf=input/test_pbta.single.vqsr.filtered.vep_105.vcf \
--filter_criteria='INFO/AF>=0.2 INFO/DP>=15 (gnomad_3_1_1_AF_non_cancer<0.01|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"

AF should be filtered for, but it is not: 

Filtering VCF...
vcf file: input/test_pbta.single.vqsr.filtered.vep_105.vcf 
cmd:  bcftools view -f 'PASS,.' input/test_pbta.single.vqsr.filtered.vep_105.vcf | bcftools filter -i 'INFO/DP>=15' | bcftools filter -i '(gnomad_3_1_1_AF_non_cancer<0.01|gnomad_3_1_1_AF_non_cancer=".")' > ../results/test_pbta.filtered.vcf

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