split step does not work correctly 1.13.15

[Liyang-Zhang]

I am using the Caveman 1.13.15 which is part of the dockstore-cgpwxs cantainer.

Instead of dividing the chromosome into sections, the split step just output the whole chromsome. The same issue happened when using cgpCaVEManWrapper.

ngularity exec $IAMGE_NAME caveman setup \ -t ${tumor} \ -n ${normal} \ -r ${genome_19}.fai \ -g ${introns_bed} \ -f ${working_dir} \ -c ${working_dir}/caveman.cfg.ini \ -l ${working_dir}/splitList \ -a ${working_dir}/alg_bean

not split chromosomes correctly

singularity exec $IAMGE_NAME caveman split \ -i 2 \ -f ${working_dir}/caveman.cfg.ini

The reference is GRCh37_ucsc, and the splitList got from looks this: $ cat splitList.chr1 chr1 0 249250621

Any advice will be appreciated.

[rulixxx]

Hi Liyang,

I think it's supposed to work like that: one index per chromosome. Instead of using CaVEMan directly, take a look at the Perl wrapper:

https://github.com/cancerit/cgpCaVEManWrapper

It should simplify the launching of analyses, you just specify the number of threads to use (along with the other arguments) and it should carry out all the steps for you.

Raul

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From: Liyang-Zhang @.> Sent: Tuesday, February 15, 2022 2:08 AM To: cancerit/CaVEMan @.> Cc: Subscribed @.***> Subject: [cancerit/CaVEMan] split step does not work correctly 1.13.15 (Issue #108)

I am using the Caveman 1.13.15 which is part of the dockstore-cgpwxs cantainer.

Instead of dividing the chromosome into sections, the split step just output the whole chromsome. The same issue happened when using cgpCaVEManWrapper.

ngularity exec $IAMGE_NAME caveman setup -t ${tumor} -n ${normal} -r ${genome_19}.fai -g ${introns_bed} -f ${working_dir} -c ${working_dir}/caveman.cfg.ini -l ${working_dir}/splitList -a ${working_dir}/alg_bean

not split chromosomes correctly

singularity exec $IAMGE_NAME caveman split -i 2 -f ${working_dir}/caveman.cfg.ini

The reference is GRCh37_ucsc, and the splitList got from looks this: $ cat splitList.chr1 chr1 0 249250621

Any advice will be appreciated.

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[keiranmraine]

Hi, your output suggests you have chromosomes prefixed with chr. The GRCh37 reference bundle provided doesn't have this prefix and will not function correctly without intervention as the system expects the reference in the bundles to be used for mapping.

[Liyang-Zhang]

Thank you all for your help.

I made a mistake when preprocessing the input tumor and normal bam files. CaVEMan Split works well after I changed the input bam files, though I don't think Split step uses the bam files. Anyway, thanks a lot.

$ head splitList.chr1 chr1 0 3397173 chr1 3397173 9501589 chr1 9501589 12802072 chr1 12802072 18808336 chr1 18808336 22974185

[Lillianwu0314]

Hi Liyang,

I'm having the exact same issue with caveman-split. My chromosomes also begin with the chr prefix like yours. I was wondering how you processed your bam files to get this to work?