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

[Freddi Scheib]

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.

Thanks!

Freddi Scheib

--
Freddi Scheib
PhD Student
University of Cambridge
Division of Biological Anthropology

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