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Old 07-16-2015, 10:12 PM   #1
anyone1985
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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 http://www.ncbi.nlm.nih.gov/pubmed/25673793. 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
westerman
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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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