Consensus With Mpileup
dear all,
I am running bwa aln with short seq, I can vizualized the BAM with Tablet but when I compare the vizualization and consensus produced with mpileup, there are majeur differences (no relation with the number of ngs). How could I obtain the max lenght of coverage for the consensus?
I am using the following commend for the consensus
samtools mpileup -uf ref.fa merge-sort.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
Thank
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Do you mean depth or coverage?
This should either be closed as no longer relevant, as it is not clear what op was asking (explain unknown differences between tablet and samtools or get the coverage of the consensus) and no clarification was given, or edited as supposed e.g. "How could I obtain the (maximum, why??) depth of coverage for the consensus sequence?" But even then, I don't think this makes much sense as a question.