Entering edit mode
3 months ago
Arton
▴
20
I'm trying to filter variants that have VAF<0.2. I used picard FilterVcf, bcftools filter, and tried to use GATK VariantFiltration, and neither of these worked. picard and bcftools only filter a portion of variants but I still get a long list of variants with VAF<0.2 labeled as "PASS". I haven't figured out how to use GATK VariantFiltration for VAF. Any help to figure out the problem would be greatly appreciated. Here are my codes:
java -jar picard.jar FilterVcf \
I=input.vcf
MIN_AB=0.2 \
O=output.vcf
bcftools filter --include '(FMT/AD[0:1])/(FMT/AD[0:0]+FMT/AD[0:1]) >=0.25 && (FMT/DP[0:0] >=10)' \
input.vcf \
--output output.vcf \
--soft-filter Filter1 \
--mode +
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For example what does mean that MIN_AB is double?
I'm not familiar enough with this bcftools syntax.
but what if there is no AD, what if both are '0', what if there is a NO-CALL at this position ? what if the variant is multiallelic ?