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[Bammds-users] Formatting BAM to work with HDGP_hg19_one_allele.txt

From: Freddi Scheib
Subject: [Bammds-users] Formatting BAM to work with HDGP_hg19_one_allele.txt
Date: Thu, 13 Nov 2014 15:13:24 +0000
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Hi there,

I'm trying to us bammds to put my aDNA .bam on a PCA (with the .txt provided just to get started). It's aligned to hg19 which has lots of chrUn_g* and other "chromosomes." I'm new to this, is there a way to use samtools to remove reads mapped to these chromosomes or extract only chr1-22, x, y, and MT?

I know how to change the header to be consistent, it's just the actual removal of reads that I have yet to figure out.

If there is an easier to format the .bam in the first place like realigning to an altered hg19 without these regions, advice on that would be appreciated as well.


Freddi Scheib

Freddi Scheib
PhD Student
University of Cambridge
Division of Biological Anthropology

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