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Thread Tools |
03-16-2011, 12:33 PM
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#1 |
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Member
Location: FL Join Date: Mar 2011
Posts: 54
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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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03-16-2011, 01:38 PM
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#2 |
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Senior Member
Location: San Diego Join Date: May 2008
Posts: 912
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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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03-17-2011, 08:49 AM
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#3 |
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Member
Location: FL Join Date: Mar 2011
Posts: 54
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Yes, I found samtools.pl in misc folder. Thanks.
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05-25-2011, 05:41 PM
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#4 |
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Member
Location: Heidelberg, Germany Join Date: Aug 2010
Posts: 39
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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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