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ssadedin / ximmer

Ximmer is a system for CNV calling on exome and targeted genomic sequencing
http://ssadedin.github.io/ximmer/
GNU Lesser General Public License v2.1
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Chromosome * is not analysable by CODEX and many more #35

Open vinzenzmay opened 4 years ago

vinzenzmay commented 4 years ago

Hello, Ximmer looks very promising, so I would really love to get it to work. Unfortunately, all tools return 1 and the very first hint of what is going wrong is:

Chromosome * is not analysable by CODEX and many more

which happens for each chromosome. I tried to run Ximmer each time on only one tool to single out the source of error, but each tool aborts at some early point. So, I guess my input is somewhat wrong. Are there any special limitations on the formats or so? Here is what I use:

  1. regular .bam files
  2. a regular bed file with gene annotations like: 1 2234359 2234599 SKI
  3. my config.groovy looks like the example from your documentation.
bam_files=[
  "/(...)/11_0348-N1-DNA1-Panel_seq1.bam",
 (...)
]
target_regions="/(...)/merged.bed"
concurrency=8
callers {
    xhmm {}
    codex {}
    cnmops {}
}

Here you can see the std out of Ximmer.

I would be really happy to use Ximmer and I am looking forward to hearing from you, Vinzenz