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-   -   Extract flanking sequence of SNP call (http://seqanswers.com/forums/showthread.php?t=45258)

JdeBruin 07-24-2014 05:49 AM

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

westerman 07-24-2014 06:03 AM

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.

swbarnes2 07-24-2014 04:06 PM

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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