Re: [Seqan-dev] splazers cigar mismatch

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

Dear Tina,

could you provide us with the whole problematic record?

Cheers,

Manuel

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From: Tina Hu [t.hu@celmatix.com]
Sent: Tuesday, June 19, 2012 9:13 PM
To: seqan-dev@lists.fu-berlin.de
Subject: [Seqan-dev] splazers cigar mismatch

Hi,

I get the following error from snp_store (on output from splazers):

WARNING! Read TESTING: cigar alignment length does not match genome coordinates. Discarding read..

I'm fairly certain this error stems from splazers as the alignment length computed from the cigar string does not match the start and end match position (off by 1 bp). Interestingly, when I truncate 300 bps same sequence from 478 bps to 178 bps, the cigar string appears to be correct. Note that 32M is now 31M which is the correct length.

cigar of the longer sequence (478 bps): 

14M1I206M1I2M1I35M1D45M1D3M1I147M1D32M

cigar of the truncated sequence (178 bps):

147M1D31M

Has anyone else encountered this issue and is there a fix?

Thanks!

Tina

--
Tina Hu, Ph.D.
Bioinformatics Scientist
Celmatix, Inc.
1 Little West 12th St.
New York, NY 10014
917.426.2878

www.celmatix.com

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