[mira_talk] Re: haplotype phasing
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 4 Feb 2014 20:26:17 +0100
On 04 Feb 2014, at 19:29 , Adrian Pelin <apelin20@xxxxxxxxx> wrote:
> I am attaching a figure with obtained results. On the left I have the PCR
> clones that I sequenced, the number in parenthesis is the number of clones
> that had that specific haplotype. On the right I have 2 mira haplotypes
> produced from small contigs, smaller than 1.5kb. As you can see the second
> one is fine, it is the same 2nd one from the left figure. The first one made
> by mira however, seems to be a combination between #3, than #4 or #5 and than
> #1.
It’s not only highly polymorphic, the naming of the contig also suggests it is
highly repetitive. This is always a problem, and in repeats all MIRA can give
is a best guess as there is really no good way to ensure that more distantly
occurring "SNP-loci” really belong together.
> […]
> Would be very neat if MIRA could build variants and their respective
> frequencies for highly polymorphic loci.
In case you have Illumina data, you might try a couple of dirty tricks to
improve things (but this might also worsen the results): extract the reads from
the assembled contigs, reassemble them with highly stringent parameters like
-AL:mrs=95 -CO:rodirs=1 … maybe that’ll work.
B.
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