number of bam files for comparison
Opened this issue · 2 comments
ibseq commented
Hi all,
is the comparison done only two bam files at the time? can we add a longer list?
thanks
ibseq
DrYak commented
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 commented
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 ***@***.***> 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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