Warning : given vaf >> vaf in config. wrong vaf threshold ?

[dbhayal9]

I am using --vaf 5 --maf 0.001 --minDepth 50 --minAltDepth 2, but its throwing an error like "Warning : given vaf >> vaf in config. wrong vaf threshold ?". if i set --vaf 1 or less then 1 then its worked. but i want to filter variants those have vaf < 5%

please give a solution if someone resolved it Thanks

[nservant]

Hi @dbhayal9 Could you check in your VCF file if the VAF is expressed as decimal ? ie. 5 or 0.05 ?

[dbhayal9]

Hi @nservant, Thank you for your quick reply, yes its in decimal. if i want to filter the variants those have <5% frequency then can i set --vaf value 0.5?

for better understanding i attached vcf file one row.

Thanks

[nservant]

So if you VAF is encoding as floating value, you must set --vaf 0.05