I am using freebayes to do variant calling in my polyploid species (with ploidy 2 anyway). Before filtering I was looking at the bam file alignment and a vcf file. Could you, please explain what does alleles
2/2, 0/2, 1/2 means?
0/0 is reference allele,
1/1 alternative and
0/1 heterozygote? Because if I filter for biallelic alleles,
2/2, 0/2, 1/2 will be removed, although in bam file I can see a very nice high quality SNP which in vcf results as
Moreover, in the situation like this, even if there is only one reference allele with a high mapping quality freebayes would result in a 0/1 call. Any suggestions/explanations? image here