I have BAM files of some ancient genomes (for example: 17X), authors mentioned in the paper that they genotyped all genomes individually using samtools (v1.3.1) mpileup –C50 and bcftools (v1.3.1) using the consensus caller. Briefly, the steps are as follows:
- Run samtools mpileup with the -C parameter set to 50 and only included sites with a depth of coverage greater than 1/3 the average depth and lower than 2 times the average depth.
- Filtered out variant calls with a phred posterior probability lower than 30.
- Filtered out variants with significant strand and/or end distance bias (p<1e-4) or located within 5 bp of each other.
- Discarded heterozygote calls if allelic balance for the minor allele was less than 0.25.
My initial command-line is:
samtools mpileup -C50 -uf ref.fa aln.bam | bcftools call -cO v -o study.vcf
I have little idea to design the simple samtools command-line with bcftools piping consensus caller but don't know how to apply filters.. can anyone please help me in command-line design.
Thanks a lot!