1. Community
2. Other
3. --minimum-allele-fraction does not work, vcf output is not filtered properly

I'm using it for viral variant calling and in my circumstance, I need to set more criteria based on ground truth data we've been studying. The command line options are available whether it's Filter...

• View comment
• Hiral Desai
• June 12, 2023 15:37
• 0 votes

1. Community
2. Other
3. --minimum-allele-fraction does not work, vcf output is not filtered properly

thank you, why is the argument available then? I also tried it for FilterMutectCalls and it does not work as intended. The expected results don't filter according to my set AF or AD.

• View comment
• Hiral Desai
• June 12, 2023 15:04
• 0 votes