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Old 01-23-2015, 01:13 PM   #1
Carlo
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Location: Stanford, CA, USA

Join Date: Oct 2010
Posts: 4
Default Tool for parsing mismatches out of a SAM file...

Hi all, I'm looking for a tool or PERL module that could take each line from a SAM file and parse the CIGAR + MD strings to output the genomic coordinates of all mismatches (specifically SNPs). I know of multiple tools that will tally up the number and type of mismatches at each position in a genome, but what I need is the reference position of all SNPs within each pair of mates in my SAM files.

I can write a PERL script to do this, but I'm hoping that I'm not the first person to encounter this issue!

Thanks,

Carlo
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Old 01-23-2015, 08:49 PM   #2
SNPsaurus
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Do you care if these mismatches are real or sequencing errors? I would think starting from a vcf file or pileup, derived from the sam file, would be both easier to parse and eliminate many of the sequencing artifacts.
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Old 01-24-2015, 01:13 AM   #3
lindenb
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I wrote SAM2Tsv : https://github.com/lindenb/jvarkit/wiki/SAM2Tsv

Code:
$ java -jar dist/sam2tsv.jar -A  \
    -r samtools-0.1.18/examples/toy.fa 
      samtools-0.1.18/examples/toy.sam
r001    163 ref 0   T   .   7   T   M
r001    163 ref 1   T   .   8   T   M
r001    163 ref 2   A   .   9   A   M
r001    163 ref 3   G   .   10  G   M
r001    163 ref 4   A   .   11  A   M
r001    163 ref 5   T   .   12  T   M
r001    163 ref 6   A   .   13  A   M
r001    163 ref 7   A   .   14  A   M
r001    163 ref 8   A   .   .   .   I
r001    163 ref 9   G   .   .   .   I
r001    163 ref 10  A   .   .   .   I
r001    163 ref 11  G   .   .   .   I
r001    163 ref 12  G   .   15  G   M
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