I have used SAMtools Version=1.2+htslib-1.2.1 for SNP calling (History option 66 in Trinity 2). The output which I have obtained is something which I am unable to understand, I have used SAMtools older version which gave me output very different from what I have obtained. Can you please help me in this direction
My questions are
1) Why is the QUAL for all samples 0??
2) Why is the column on alternate allele with X.
3) How do I filter the output in the form of SGB??
Looking forward for your help.