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Old 06-03-2011, 06:28 AM   #1
sdarko
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Location: Bethesda, MD

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Default Are there any alignment programs that take SNPs into account during alignment?

I was recently looking through some mRNA-Seq alignments in IGV that I made with TopHat and I loaded up the SNP track to compare some alignment mismatches to known SNPs. I was looking at it and it occurred to me that, to an alignment algorithm aligning against a reference genome, SNPs and mismatches would look the same so that a read that had a real SNP and a base call error would look like a read with two mismatches and (possibly) wouldn't align.

So, are there any alignment programs that take SNPs into account during alignment by, say, using SNP tracks as an optional input?
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Old 06-04-2011, 02:41 AM   #2
Simon Anders
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How about GSNAP? You can pass it a list of SNPs in addition to the reference.

Thomas D. Wu and Serban Nacu
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Bioinformatics 2010 26: 873-881
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Old 06-04-2011, 06:09 AM   #3
lh3
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gsnap, mosaik and novoalign
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