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Forum: Bioinformatics 01-23-2014, 03:41 AM
Replies: 0
Views: 1,074
Posted By msalm
Soft-clipping in Stampy

Hi there!

Does anyone have any experience with producing/retaining the soft-clipping signature in CIGAR strings when using Stampy (v.1.0.21), using BWA alignment as input?

Cheers,

Max
Forum: General 02-19-2013, 04:29 AM
Replies: 5
Views: 2,249
Posted By msalm
For SNV calling, I would also highly recommend...

For SNV calling, I would also highly recommend VarScan2 (http://www.ncbi.nlm.nih.gov/pubmed/22300766). Others include SomaticSniper (http://www.ncbi.nlm.nih.gov/pubmed/22155872) and Strelka...
Forum: Bioinformatics 04-16-2012, 03:38 AM
Replies: 3
Views: 2,474
Posted By msalm
Hi there, some options are: ExomeCNV ...

Hi there,

some options are:

ExomeCNV
http://bioinformatics.oxfordjournals.org/content/27/19/2648.full

VarScan2
http://genome.cshlp.org/content/early/2012/02/02/gr.129684.111.full.pdf+html
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