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Error: Found chromosome in region file not in reference genome. Skipping #138

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@shguturu

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@shguturu

Hello! I am trying to run svaba for targeted SV detection.

The command works with Svaba v1.1.0 but with v1.2.0 it throws the following error:

"Found chromosome in region file /rtsess01/juno/home/arorak/resources/ACCESSv2_targets_coverage.100bp_padding.bed not in reference genome. Skipping.
   Caught error: regex_error
ERROR: Cannot read region file: /rtsess01/juno/home/arorak/resources/ACCESSv2_targets_coverage.100bp_padding.bed or something wrong with bam header ('chr' prefix mismatch?)"

I am using the same region file that was working with Svaba v1.1.0 so am unsure why it is not working with the new version. Is there a change that needs to be made to the region file? Thanks in advance!

Here is the command for reference:
"svaba run -G $REF_GENOME.fa -t $TUMOR.bam -n $NORMAL.bam -k $targets.bed -C 5000 -p 4 -a svaba_trial"

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