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!
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!
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