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Old 11-19-2010, 05:08 AM   #1
mrxcm3
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Default Samtools version 1.0.7 and 1.0.10 different pileup

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??
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Old 11-19-2010, 07:24 AM   #2
nilshomer
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Quote:
Originally Posted by mrxcm3 View Post
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]
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