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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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Should be an existing file #111

Open mdbarnesUCSD opened 2 years ago

mdbarnesUCSD commented 2 years ago

I am running using the docker container with singularity:

When I run the following command: singularity exec brass_v6.3.4.sif brass.pl -c 2 -o ${output_dir} -t ${t_bam} -n ${n_bam}

I receive the following message:

Option 'tumour' ([tumor/file/path) should be an existing file.

The tumor file does exist and is found at the specified path. I see on the README that it says the following:

BRASS requires accurate information regarding the insert size distribution and expects to find a .bam.bas file co-located with the .bam's. These can be generated by the bam_stats program included in the PCAP-core project. If you use bwa_mem.pl to map your data (same repository) then this file is generated automatically for you.

Could you please clarify if I need to have any other files in the same directory as my bam files, or is this handled by the script?

Thank you very much for your help!

AndyMenzies commented 2 years ago

Hi

You need the .bam.bas file to exist along side the .bam file, just as the .bam.bai index file also has to live in the same place.

Brass will not create the .bam.bas file or you, you need to run the bam_stats.pl script found the PCAP-core project.

Andy