[Gmod-ajax] JBrowse Alignment2/SNPCoverage tracks

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[Gmod-ajax] JBrowse Alignment2/SNPCoverage tracks

Keiran Raine
Hi,

I just wanted to know if the BAM tracks use the MD tag when calculating which positions differ from reference?

I only ask as GBrowse originally didn't use the MD tag which was a bottle-neck.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Rese arch Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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Re: JBrowse Alignment2/SNPCoverage tracks

Robert Buels-2
On 11/14/2013 03:44 PM, Keiran Raine wrote:
> I just wanted to know if the BAM tracks use the MD tag when calculating
> which positions differ from reference?

Yes. It actually requires the MD tag to show mismatches.


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