Hi all,
Has anyone come across a way to get information about the location of a snp within the reads? I have the usual bam/sam/pileup files.
For example,
r1: GAG
r2: GGG
r3: AGA
ref: AAAGGGTTTT
In this very contrived example that was hopefully preserved by the editor we would have a single snp represented at pos 2 in read 1, and pos 3 in read 3 . What I am looking for is a way to get that information that says this snp is at pos 2 in r1, and position 3 in r3 from bam/sam/pileup files.
Does anyone know of a tool that can do this?
thanks for any help.
Has anyone come across a way to get information about the location of a snp within the reads? I have the usual bam/sam/pileup files.
For example,
r1: GAG
r2: GGG
r3: AGA
ref: AAAGGGTTTT
In this very contrived example that was hopefully preserved by the editor we would have a single snp represented at pos 2 in read 1, and pos 3 in read 3 . What I am looking for is a way to get that information that says this snp is at pos 2 in r1, and position 3 in r3 from bam/sam/pileup files.
Does anyone know of a tool that can do this?
thanks for any help.
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