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Correctly split hg38 HLA contigs during configuration #12
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Chris;
I've been testing manta on hg38 and ran into a small issue with HLA contig parsing fixed here. There is also a downstream issue which I can work around with more details below. With these two fixes in place we can run on 38 without any issues and get similar sensitivity/precision to build 37.
When testing manta on hg38 full from the 1000 genomes distribution,
there are problems handling the HLA contigs, which contain colons:
HLA-A*01:01:01:01
.Configuration fails with:
when splitting the names from the BAM tags. This small fix resolves the
problem. When running, there is also a downstream failure with a similar
problem trying to parse ranges in names with colons:
I worked around this by excluding HLA regions from manta, with
--region
but just as an additional related source of issues.