Hiral Desai
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Activity overview
Latest activity by Hiral Desai-
Hiral Desai commented,
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...
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Hiral Desai commented,
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.
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Hiral Desai created a post,
--minimum-allele-fraction does not work, vcf output is not filtered properly
REQUIRED for all errors and issues: a) GATK version used: 4.2.6.1b) Exact command used: gatk Mutect2 -R ref_seq.fasta -I snp50-x3.sorted.rg.MD.bam --minimum-allele-fraction 0.05 -O snp50-x3.sorted...
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Hiral Desai created a post,
Mutect2 set variant filter in command line
I am using mutect2 for variant calling (The Genome Analysis Toolkit (GATK) v4.2.6.1). What command line option can be used to set variant frequency to 1% in mutect2 command line to decrease false p...