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Old 06-30-2011, 12:11 PM   #1
Location: helsinki

Join Date: Jun 2011
Posts: 54
Default How to separate individual sample variants from multiple samples

Hi all,

I have paired-end reads of multiple samples from one illumina run. I have aligned them using BWA and trying to call variants using SAM tools. I used the pileup command to generate SNPs /Indels form the sorted BAM file, where i got the variant list from all samples.

I read in the manual that @RG header has something to do with sample names(which im not clear), but i couldnt find @RG header in my file. Any help from anyone would be greatly appreciated.
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