Re: [Seqan-dev] SNP and Indel location

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Ananth,

This is currently not possible using mason.

I would also recommend to use an external tool for simulating SNPs since mason does not do indels that keep the reading frame (i.e. most lengths should be multiples of 3) etc. For read mapping, this is sufficient, for SNP detection, it is most probably not.

*m

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From: Anantharamanan R [ananthr@ncbs.res.in]
Sent: Friday, April 13, 2012 12:21 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] SNP and Indel location

Dear All,

              I am simulating illumina reads with  -hs, -hi (default rate 0.001). I want to know where exactly these variants are introduced (Location) into my genome during simulation. It would be really great if somebody help me to trace this.

Regards
Ananth