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Old 09-20-2011, 11:31 AM   #1
prbndr
Junior Member
 
Location: United States

Join Date: Sep 2011
Posts: 5
Default find all snps/indels

is there a good way to find all the snps and indels (or just deletions in the read) from a sam file? has anyone written an MD tag parser that can do this? i tried a workaround by using the samtools variant caller, but that filters a lot of the snps out from my sam file -- i can't get it to output every single snp and indel. any ideas?
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