Hello! I am trying to extract the consensus sequence from a sorted BAM file that was got after alignment. The commands I will be using are:
bcftools mpileup -Ou -f Aedes-aegypti-LVP_AGWG_CHROMOSOMES_AaegL5.fa AEB21A.bam | bcftools call -mv -Ob -o AEB21A_calls.bcf bcftools index AEB21A_calls.bcf cat Aedes-aegypti-LVP_AGWG_CHROMOSOMES_AaegL5.fa | bcftools consensus AEB21A_calls.bcf > AEB21A_consensus.fa
bcftools mpileup has a default of 250 for the
--max-depth option, which I want to change. I am not sure what would be a good value to set. I am working with a eukaryotic insect genome of around 1.28 Gb.