Hi, I'm working on polypoid plant. Where using samtools and BCF tools to call SNP. We realize that bcftools have difficulty calling some simplex genotype and i would like doing it on my own. Is there a way to extract the number of reference and alternative allele from a mpileup format?
Thanks,
Gabrielle
It might be worth checking out other variant calling software. For example I have been using SNVer for pooled and non diploid data. http://snver.sourceforge.net/