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Old 07-16-2015, 10:12 PM   #1
Location: shanghai, chia

Join Date: Mar 2009
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Default reads mapping to each strand?

I read some literatures about call sv with samtools and noticed a filter to remove the candidate sv based on the reads mapping to each strand. for example, this paper I'd not know how to set up this filter within samtools. Please help me out. Besides, I think the Mycobacterium is haploid. Is it right to call the sv using samtools? Maybe they should use gatk or freebayes with haploid model.
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Old 07-17-2015, 09:51 AM   #2
Rick Westerman
Location: Purdue University, Indiana, USA

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Flag 0x0010 (r) is the strand of the query; true if on the reverse strand. You can use samtools to filter on that flag.

As for calling the SV with Samtools, why not? GATK may arguably have a better model but Samtools can be good.

Last edited by westerman; 07-17-2015 at 09:51 AM. Reason: Spelling
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