Samtools pileup and mpileup for one bam file generating different output

[var]

Hi,

I have an aligned BAM file and I need to get a detailed list of the all the snp poisitions (Which includes the freqeuncy of the alternate alleles as well at each position). Before implementing any program, I tried generating a pileup for the BAM file.

Now I tired generating pileups using the SAMtools pileup (the deprecated one as they say) as well as using Mpileup (the current version). Mpileup, as I understood, is just a pileup for multiple BAM files??? and so I was expecting the pileups generated by the two programs to be exact! However, it isn't the case!

The list of positions being generated are different!

I plan to use Varscan on the pileup format but I am not sure which Pileup to take.

I think I am missing on something real improtant here and would really appreciate someone helping me!

Thanks!

[colindaven]

We haven't used pileup since it became deprecated several years ago.

I would definitely use mpileup.

[LiLin]

if you try samtools pileup,you may see

Warning: Please use the `mpileup' command instead `pileup'. `Pileup' is deprecated!

so please use mpileup,

[dkoboldt]

As the others said, use mpileup but be aware that there are differences between the two commands, most notably that BAQ adjustment is turned on by default in mpileup, which affects base qualities. See my blog post on 5 things to know about SAMtools mpileup.