Hi everyone, I am working with ancient DNA, and I'd like to call a consensus fasta file from my mapped data (BAM). Since it is ancient DNA it is often happening that there are missing, or poorly covered positions in my BAMs, so when I want to call a consensus fasta from vcf I also want to call the missing positions as N's, and the poorly covered (DP=3>) as... something reliable. I am using bcf/samtools for the task but I have no idea, how to call missing positions for the fasta, or how to make a threshold for non-mutant positions. I know, there is schmutzi for mitochondrial data, but somehow I cant use that one (I would appreciate help for that too). Thanks in advance!
@gerberd1990 I wrote schmutzi's endoCaller. It calls a consensus for mt data and can account for present-day human contamination and damage due to deamination. But, it is only for haploid data (mitochondrial or chloroplast) but not for nuclear data. Let me know if you need help using it.