Samtools pileup Consensus with 0.1.12a version

[srividya]

Hello,

I am using samtools 0.1.12a version for pileup consensus variant calling (-vc). I have aligned the reads with Soap Aligner and I am trying to call the consensus SNPs. Though, the pileup(only -f option) for the bam file is getting generated, I am unable to generate the consensus (-vc option) with it. I checked the CIGAR and also the sam file. They are pretty much looking normal. Can anyone tell what might be the problem?

Thanks,
Srividya

[nilshomer]

Post a small set of reads that give this problem. Also, consider moving to the latest version of samtools, which uses "mpileup" instead of "pileup".