number of bam files for comparison

[ibseq]

Hi all, is the comparison done only two bam files at the time? can we add a longer list?

thanks ibseq

[DrYak]

Yes, you can: the -a / --alignments can take an arbitrarily large number off SAM/BAM/CRAM alignment files.

(Though in our own case, we mostly use it with the -s / --samples options, as we process our samples upstream with V-pipe).

Note that each sample will be processed sequentially (there's no built-in parallelism in the cooc-mutbamscan executable).

If your collection of samples if very large, you can split it into multiple jobs, and then simply merge the YAML or JSON output.

[ibseq]

vpipe is a variant caller, how do you generate the bam files. will any from the artic pipeline (illumina or ONT) will work? thanks ibseq

On 9 Feb 2021, at 16:43, DrYak notifications@github.com wrote:

 Yes, you can: the -a / --alignments can take an arbitrarily large number off SAM/BAM/CRAM alignment files.

(Though in our own case, we mostly use it with the -s / --samples options, as we process our samples upstream with V-pipe).

Note that each sample will be processed sequentially (there's no built-in parallelism in the cooc-mutbamscan executable).

If your collection of samples if very large, you can split it into multiple jobs, and then simply merge the YAML or JSON output.

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