[mira_talk] Re: Mapping back to the assembly!
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 20 Nov 2013 21:41:35 +0100
On 20 Nov 2013, at 16:33 , Adrian Pelin <apelin20@xxxxxxxxx> wrote:
> I was amazed, but I found 76 loci, that had 0 observations for their
> Reference allele (what MIRA build), and a bunch of observations for the
> alternate allele. So essentially, the Alternate allele had 100% frequency,
> indicating these to be Homozygous SNPs.
Easy test to see whether MIRA goofed or not: take a 31bp kmer right across the
suspected SNP and use that with mirabait to grep out reads with that variant to
do a mini-assembly. Once for every variant.
> This shouldn't be happening, and what this tells me is that either MIRA did
> not call the basepairs properly, or the mapping algorithm mapped the reads
> differently than what MIRA did when it constructed these contigs. I believe
> the latter to be very likely, and I wanted to use bowtie or bwa to see if the
> homozygous SNPs I find using a different mapper are in a different location
> now.
Some mappers may choose not to map repetitive reads, maybe that’s what you see?
B.
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