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I have the same question - Is it possible to change the cut-offs for number of reads supporting variant allele in the tumor sample ? What parameter controls it ? I see that there are options to do it in for the normal sample.
Yes - That's true and I have also observed the same. It creates problems when you use the file for annotations as the order of the columns is not consistent in the vcf file. I hope this can be fixed in mutect.
Ok I was able to call it as somatic by giving different values to the following parameters --max_alt_alleles_in_normal_count 6 --max_alt_allele_in_normal_fraction 0.05 --max_alt_alleles_in_normal_qscore_sum 200 However knowing the default values for…