calling variants on haploid organism
I'm curious about something I find using HaplotypeCaller on my haploid fungus. (using it with -ploidy 1)
In my vcf there are some variants with low variant allele frequency (around 50%).
for example : chr_5 522158 . C T, 34.01 . BaseQRankSum=0.529;ClippingRankSum=0.689;DP=15;MLEAC=1,0;MLEAF=1.00,0.00;MQRankSum=-0.380;RAW_MQ=18495.00;ReadPosRankSum=0.831 GT:AD:DP:GQ:PL:SB 1:5,7,0:12:64:64,0,228:3,2,3,4
Are there no filters for those kind of variants when using -ploidy 1 option? (for an haploid species I'm not supposed to find both ref and alt on the same position)
Thank you for your help,