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cancerit / BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
GNU Affero General Public License v3.0
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Generating an input bas? #96

Closed cboursnell closed 4 years ago

cboursnell commented 4 years ago

Apologies if this has been asked before or this is a stupid question, but how do you generate a .bas file for an input .bam file?

keiranmraine commented 4 years ago

If you are using the container from quay.io (needs adding to readme/wiki) you can call bam_stats which is from one of the dependencies:

https://github.com/cancerit/PCAP-core/wiki/Scripts-Generic#bam_stats-c

If you have a native install bam_stats would have been installed as part of the PCAP-core dependency.