Question: What Is The Difference Between Samtools Mpileup And Pileup
3
gravatar for Ian
8.0 years ago by
Ian5.3k
University of Manchester, UK
Ian5.3k wrote:

As of samtools 0.1.8 'mpileup' appears to have superseded 'pileup' for variant detection. The samtools website now has pileup as deprecated.

So i am wondering whether i should repeat my recent SNP/INDEL calling with mpileup? But does anyone know what the improvements are using mpileup?

For those who don't already know 'pileup' and 'mpileup' can be used to create a consensus sequence using NGS mapped reads relative to a reference genome, but can also highlight variants relative to the reference.

indel pileup samtools mpileup snp • 13k views
ADD COMMENTlink modified 8.0 years ago by lh331k • written 8.0 years ago by Ian5.3k
7
gravatar for lh3
8.0 years ago by
lh331k
United States
lh331k wrote:

For single-sample SNP calling, they differ little. Pileup uses BAQ by default, too. The major difference comes from indel calling. Mpileup implements a more advanced method. For indel calling, do not use pileup any more.

ADD COMMENTlink written 8.0 years ago by lh331k
1

Mpileup also outputs pileup.

ADD REPLYlink written 7.9 years ago by lh331k

It seems pileup is going away in the next release. The pileup raw output was still very useful (read coverage among others). If that feature goes away, what tool can be used as a replacement? An alternative would be to write your version. I wanted to check before moving in that direction.

ADD REPLYlink written 7.9 years ago by Drio910
3
gravatar for Pablo
8.0 years ago by
Pablo1.9k
Canada
Pablo1.9k wrote:

Indeed, mpileup is a pileup that supports multiple samples and the old pileup is deprecated.

Mpileup by default uses a new algorithm (BAQ). The Snp calling is now done by BcfTools, which (I think) also made some improvements.

Since generating mpileup/bcf/vcf is not such a long process, I'd recommend re-calculating the calls.

ADD COMMENTlink written 8.0 years ago by Pablo1.9k
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