Mosaics for bam files

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SR

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Sep 28, 2012, 4:05:53 AM9/28/12
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Hello,

I was wondering if you have a script to preprocess BAM files for single end data (aligned with BWA).

Thank you!

Regards,

Sigrid

Dongjun Chung

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Sep 29, 2012, 1:46:39 PM9/29/12
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Hi Sigrid,

mosaics does not support bam file formats as its direct input but it supports sam file formats instead. There are popular tools to convert bam files to sam files, including samtools:

http://www.biostars.org/post/show/1701/how-can-i-convert-bam-to-sam/
http://samtools.sourceforge.net/
https://main.g2.bx.psu.edu/root?tool_id=bam_to_sam

You can convert bam files to sam files using these tools and then process the output sam files using mosaics package.

Thanks,
Dongjun
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