New GATK user here. Using mutect2 to detect somatic mutations in a CRISPR/Cas9 edited population of plant clones. Sequencing is targeted illumina short read PE using bait probes for pull-down. I know this is a very unique use of this program but it seemed ideally suited to the task.
Running GATK 184.108.40.206 on terra and GATK 220.127.116.11 locally. Running mutect2 in normal/tumor mode. Mutect2 runs to completion no problem.
My issue concerns FilterMutectCalls. I would like to use the --unique-alt-read-count argument to increase the stringency and eliminate sites that are scored PASS but have only a few unique reads supporting the alternative allele. When I run FilterMutectCalls using --unique-alt-read-count with values of 1,10,50,100,1000, there is no change in the sites that reach a PASS call. Manual inspection of PASS sites in a browser shows some sites should be eliminated based on this argument. When I use the --min-allele-fraction argument I am successfully able to reduce PASS calls based on the allele frequency. Running mutect2 locally in GATK 18.104.22.168 and FilterMutectCalls locally in the same version produces the same result. When running FilterMutectCalls with --unique-alt-read-count I receive no errors and all the expected output files.
How do I get the --unique-alt-read-count parameter to function in FilterMutectCalls?
Thanks very much for your time!
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