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Old 02-15-2013, 08:48 AM   #1
ramirob
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Location: Vermont

Join Date: Apr 2012
Posts: 14
Default Comparing sequences between themselves

Hello,

We ran an experiment where we sequenced WT and mutant isolates from the same particular organism. We have aligned these samples to reference (using BWA) and then found SNPs (using GATK). However, aside from identifying SNPs by comparing to reference, we would like to compare the aligned samples between themselves to look for important differences (eg. WT to Mutant samples). Does anyone have any suggestions on how to approach that? It can certainly be done indirectly by comparing the SNP calls, but I was wondering if there is any existing software that does something like that (e.g. find SNPs between aligned samples as opposed to find SNPs when compared to reference).

Thanks in advance,
Ramiro
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