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Old 03-16-2011, 12:33 PM   #1
slny
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Default How to get consensus sequence from .sam file?

I'm trying to get consensus sequence from sam file according to the instruction from samtools website as below.

samtools pileup -cf ref.fa aln.bam | samtools.pl pileup2fq -D100 > cns.fastq

However, there is actually no samtools.pl. Is there any way I could get the consensus sequence from sam file?

Thanks
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Old 03-16-2011, 01:38 PM   #2
swbarnes2
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In the latest release, its in the misc folder. And I think the latest release has a vcf2fq subroutine in vcfutils, but it's slow because you have to make a massive all-points .bcf file, and neither program will correct for indels.
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Old 03-17-2011, 08:49 AM   #3
slny
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Yes, I found samtools.pl in misc folder. Thanks.
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Old 05-25-2011, 05:41 PM   #4
dagarfield
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I think you may find this link helpful
http://samtools.sourceforge.net/mpileup.shtml

Pileup is now depreciated.
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