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Old 07-24-2014, 06:49 AM   #1
JdeBruin
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Location: South Africa

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Default Extract flanking sequence of SNP call

Hi all.

I have mapped sequencing data to a reference using BWA and called SNP using samtools mpileup and generated a vcf using bcftools. What I would like to achieve is to extract the SNP along with a 35base flanking sequences. I would appreciate any help with this.

Thanks
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Old 07-24-2014, 07:03 AM   #2
westerman
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bedtools always comes to mind when asking questions like "how to extract sequence". It should be easy to convert the VCF single coordinate into the start & end coordinates for a BED file (Excel or other spreadsheet program or a simple Perl/Python script). Then use fastaFromBed.
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Old 07-24-2014, 05:06 PM   #3
swbarnes2
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samtools faidx, when given genomic coordinates, will make a fasta of the desired region. That another way, using software you've already got.
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