Multi-sample variant calling: simultaneous read access to all BAM files required?

Andreas Wilm

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Feb 14, 2016, 9:51:10 AM2/14/16

to GotCloud

Hi all,

I was wondering if simultaneous read access to all BAM files is required for multi-sample variant calling. Or is it possible to do this only with the glf and other derived files? Ideally I'd like to able to remove all BAM files due to space constraints. Any pointer would be helpful.

Many thanks,
Andreas

Hyun Min Kang

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Feb 15, 2016, 11:13:36 AM2/15/16

to Andreas Wilm, GotCloud

Hi Andreas, unfortunately, it is not straightforward with current implementation. BAM access is needed for extracting features during filtering step.

Thanks,

Hyun.

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Andreas Wilm

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Feb 15, 2016, 9:29:07 PM2/15/16

to Hyun Min Kang, GotCloud

Thanks Hyun. One more question: is any such feature planned and if
yes, what's the timeline?

Many thanks.
Andreas

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Hyun Min Kang

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Feb 15, 2016, 10:24:22 PM2/15/16

to Andreas Wilm, GotCloud

We do not plan such a feature. Iterating BAM twice would be quite useful in many cases. If you use CRAM format with aggressive quality binning, you can get the size of sequence read of deep genomes to ~15GB, which is not too bad.

Andreas Wilm

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Feb 15, 2016, 10:26:06 PM2/15/16

to Hyun Min Kang, GotCloud

Thanks again

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