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Possible bug in SelectVariants tool
Dear GATK experts,
I have done variant calling on 384 potato samples following, mostly, GATK best practices and have applied hard filters to select SNPs for further usage. However, I am noticing that '--max-nocall-fraction', '--max-nocall-number' and '--max-fraction-filtered-genotypes' arguments for 'SelectVariants' are not working properly. I have tried with various cutoff settings and every time I am observing SNPs with a much larger number of genotypes (~246 out of 384) with 'no call' than the set thresholds. I have searched the forum first but couldn't find any relevant threads. I am using the latest GATK version (18.104.22.168). I am attaching three example sets of (1) log files (2) subset vcf files and (3) vcf index file for the three main vcfs. I would appreciate if you could provide any feedback on this issue and/or if this behaviour has been observed by some other users also.