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Correctly split hg38 HLA contigs during configuration #12
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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: ``` CONFIGURATION ERROR: Reference fasta and 'Normal' BAM/CRAM file conflict on chromosome: 'HLA-A*01' ``` 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: ``` FATAL_ERROR: EstimateSVLoci EXCEPTION: ERROR: can't parse bam_region [err 1] HLA-A*01:01:01:02N:1-3291 ``` I worked around this by excluding HLA regions from manta, with `--region` but just as an additional related source of issues.
ctsa
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Correctly split hg38 HLA contigs during configuration
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Thanks for pointing out the issue Brad, I'll merge this with some other changes that make handling these names automatic -- we have v0.29.0 with full CRAM support just about ready so I'll add this into that release. |
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Issue should be fully addressed in today's update: https://github.com/Illumina/manta/releases/tag/v0.29.0 |
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Brilliant, thanks Chris. v0.29.0 works great. Thanks for looking at this so quickly and for all the great work on Manta. |
x-chen
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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
--regionbut just as an additional related source of issues.