Hi,
I used Bowtie to align a solid read to the human genome, and now I'm trying to use samtools to call snps. When I use the pileup function, I get tons of snps, most due to a polymorphism (poly-c) in which there is a difference between my read and the reference. As samtools doesn't recognize this I get tons of snps from that point onwards.
I would appreciate any help on the matter.
Thanks,
Eyal
I used Bowtie to align a solid read to the human genome, and now I'm trying to use samtools to call snps. When I use the pileup function, I get tons of snps, most due to a polymorphism (poly-c) in which there is a difference between my read and the reference. As samtools doesn't recognize this I get tons of snps from that point onwards.
I would appreciate any help on the matter.
Thanks,
Eyal
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