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GCNV ploidy_priors has hard coded contig names #489
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Nicolai-vKuegelgen
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This reverts commit 4fc47cc.
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The previous fix introduced a new bug, because the {} brackets in the regex are first pasred by python/snakemake string formatting |
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Describe the bug
The GCNV model building requires prior values for contigs (=chromosome), which are hard coded into the corresponding snappy wrapper. However, the names of the contigs can be different depending of the soruce and version of the chromosome build on is using (i.e. GRCh37 vs GRCH38).
To Reproduce
Steps to reproduce the behavior:
Expected behavior
The file with ploidy_priors that snappy creates needs to have contig names matching the used reference files.
Additional context
This is the file which hardcodes the priors and currently contig names
https://github.com/bihealth/snappy-pipeline/blob/main/snappy_wrappers/wrappers/gcnv/contig_ploidy/wrapper.py
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