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Old 07-24-2014, 05:49 AM   #1
Location: South Africa

Join Date: Jun 2013
Posts: 25
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.

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