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-   -   find all snps/indels (http://seqanswers.com/forums/showthread.php?t=14217)

prbndr 09-20-2011 11:31 AM

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?

swbarnes2 09-20-2011 11:41 AM

samtools and GATK, as just two examples, will parse .bam files, and output variants.

prbndr 09-20-2011 11:43 AM

but they seem to filter variants. how do i completely turn the filter off and output every single variant present in the sam file?


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