RePlow with Non-Human Data

[Jesse Gibson]

Hi, I'm curious if it is possible to use this tool with non-human (invertebrate) data? I have tried running the jar file providing the reference genome (-r), bed file of target regions (-T) and a list of bam files for each of the replicate samples (-b) and I get the following error

Rearrange target regions ... Exception in thread "main" java.lang.IllegalArgumentException: Cannot add interval chr1:3745825-3745942    +       ., contig not in header
        at htsjdk.samtools.util.IntervalList.add(IntervalList.java:94)
        at replow.TargetRearrangement.rearrangeTargetsForErrorProfliing(TargetRearrangement.java:196)
        at replow.RePlow.callVariants(RePlow.java:87)
        at replow.RePlow.main(RePlow.java:34)

I'm not entirely sure where it is trying to add the interval on chr1 but it's not surprising that this would fail as my reference assembly doesn't have any contigs with that name and it doesn't show up in the bam files either. I thought perhaps providing the vcf files of candidate mutations called by Mutect2 might help so I passed a list of .vcf.gz files with the -V flag. This still threw an error but different this time

Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1
        at replow.ErrorProfileEstimator.importKeepIxnCallInfo(ErrorProfileEstimator.java:106)
        at replow.RePlow.callVariants(RePlow.java:44)
        at replow.RePlow.main(RePlow.java:34)

I thought this might be a result of the compression so I wrapped each of my files in <(gunzip -c FILE) to decompress which got rid of the index out of bounds error but once more throws the illegal argument exception from before (trying to add the interval on chromosome 1). Are there other files specific to my organism I can provide to prevent this behavior or is the tool entirely designed to work with human data? Let me know if any additional information might help

Thanks!

[Karina Lord]

Hi, I am also curious about this. Was this ever resolved?