find all snps/indels

prbndr · 09-20-2011, 11:31 AM

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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09-20-2011, 11:31 AM	#1
prbndr Junior Member Location: United States Join Date: Sep 2011 Posts: 5	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?

09-20-2011, 11:41 AM	#2
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	samtools and GATK, as just two examples, will parse .bam files, and output variants.

09-20-2011, 11:43 AM	#3
prbndr Junior Member Location: United States Join Date: Sep 2011 Posts: 5	but they seem to filter variants. how do i completely turn the filter off and output every single variant present in the sam file?