Hi,
Does anyone know of a way to straightforwardly retrieve all reads (from resequencing) that have a SNP present in them? We're generating vcf files, using bwa+gatk, and would then like to know all reads which contain a SNP listed in the vcf file. I know that I can write a wrapper that uses samtools view for a region containing a SNP, and then look at each read individually (the SNPs will be heterozygous) that maps to that location, but I wondered whether there is something that is likely faster than this, as I'd likely implement the wrapper in Perl, which will be slow for thousands of SNPs x many strains.
Cheers,
Gavin
Does anyone know of a way to straightforwardly retrieve all reads (from resequencing) that have a SNP present in them? We're generating vcf files, using bwa+gatk, and would then like to know all reads which contain a SNP listed in the vcf file. I know that I can write a wrapper that uses samtools view for a region containing a SNP, and then look at each read individually (the SNPs will be heterozygous) that maps to that location, but I wondered whether there is something that is likely faster than this, as I'd likely implement the wrapper in Perl, which will be slow for thousands of SNPs x many strains.
Cheers,
Gavin
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