Multisample BAM/multiple bam files

Davide Cittaro

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Dec 29, 2020, 7:59:02 AM12/29/20

to delly-users

Hi all,

For several reasons I have BAM files made of multiple samples (identified by ID/SM tags). I've noticed that delly warns about this:

Warning: Multiple sample names (@RG:SM) present in the BAM file!

and that the resulting bcf includes genotypes for a single sample, the first found in the BAM header. I've read that delly performs joint calling, hence is it correct to assume that the results are derived from the analysis of all reads in the BAM file?

In principle I can separate samples in different files, but since I'm not really interested in individual genotypes but only in SV definitions I'd like to know if I'm doing right.

d

Tobias Rausch

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Dec 29, 2020, 11:09:24 AM12/29/20

to Davide Cittaro, delly-users

Hi,

Each BAM file is considered as a single sample and all reads are taken into account.

Best, Tobias

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Davide Cittaro

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Dec 29, 2020, 11:57:57 AM12/29/20

to delly-users, Tobias Rausch

Excellent, that’s exactly what I needed.

Thanks

d

Sent from my iPhone

On 29 Dec 2020, at 17:09, Tobias Rausch <rausc...@gmail.com> wrote:

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