Different versions of samtools-pileup

[dg.pooja]

Hello,

** I have used pileup function with -vcf options both with samtools versions 0.1.7a and 0.1.12a

** I found the pileup output from both versions of samtools to be very different.

** Using the same aligner with exact same options, samtools 0.1.7a is giving me 452 unique SNVs and the version 0.1.12a 251 unique SNVs.

** There are 196 SNVs that are common to both versions of samtools. This is after I use varfilter with default parameters with SNP quality cutoff of 20.

** I understand that the old version of samtools use the MAQ SNP calling criteria and we have not used -A option with samtools version 0.1.12a, hence have not forced MAQ calling criteria.

*** I am confused with the data and would like to understand why there is such difference in results between the two versions of samtools.


Can any one help in this regard ?

Thank you
Pooja

[drio]

The snp caller engine has changed dramatically among those versions. Review carefully the manuals, particularly mpileup.

That being said. The overlapping events sounds a little bit low but it depends on the coverage for your project.

[swbarnes2]

Using the -B option on the new pileup command might cause it to behave more like the old pileup.

[drio]

If I am not mistaken the latest version uses the SOAP model instead of the MAQ model at the core of the snp caller. Let us know if by removing BAQ computations (-B) you get similar results to the old version.