Samtools version 1.0.7 and 1.0.10 different pileup

[mrxcm3]

Hi

When I run pileup in samtools (samtools pileup -f ref.fa input.bam > results.pileup) I get considerably less reads when using v1.0.10 than 1.0.7. For example I have a 6kb amplicon - every base has ~30% fewer reads in .0.10. The bam and ref are the same. Does the later version of samtools filter reads??

[nilshomer]

Hi

When I run pileup in samtools (samtools pileup -f ref.fa input.bam > results.pileup) I get considerably less reads when using v1.0.10 than 1.0.7. For example I have a 6kb amplicon - every base has ~30% fewer reads in .0.10. The bam and ref are the same. Does the later version of samtools filter reads??

A good place to start would be to email the samtools help list:
[email protected]