Question: Consensus With Mpileup
3
gravatar for Dunand
7.9 years ago by
Dunand30
Dunand30 wrote:

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

mpileup • 2.9k views
ADD COMMENTlink modified 5.7 years ago by Biostar ♦♦ 20 • written 7.9 years ago by Dunand30

Do you mean depth or coverage?

ADD REPLYlink written 7.9 years ago by Zev.Kronenberg11k

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.

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by Michael Dondrup46k
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