Use X/Y specific settings for deepvariant/trio #760
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config/nxf_call_snv.config
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| snv { | ||
| GRCh38 { | ||
| reference { | ||
| haploidContigs = "chrX,chrY" |
Contributor
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add chrY_KI270740v1_random?
config/nxf_call_snv.config
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| GRCh38 { | ||
| reference { | ||
| haploidContigs = "chrX,chrY" | ||
| parRegionsBed = "${VIP_DIR_DATA}/resources/GRCh38/GRCh38_PAR_20251126.bed" |
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add a doc with source or instructions how to recreate file
docs/usage/config.md
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| | cram.call_sv | true | enable/disable the detection of structural variants. disable this manually in case of non-paired-end Illumina data. | | ||
| | snv.GRCh37.reference.haploidContigs | | | | ||
| | snv.GRCh37.reference.parRegionsBed | | | | ||
| | snv.GRCh38.reference.haploidContigs | chrX,chrY | chromosomes that should be considered haploid for male samples | |
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add chrY_KI270740v1_random?
dennishendriksen
approved these changes
Dec 1, 2025
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bash test/test.shand verified that all tests passcram/complex | PASSED | 492101=completed output/cram/complex/.nxf.log
cram/multiproject | PASSED | 492102=completed output/cram/multiproject/.nxf.log
cram/nanopore_duo | PASSED | 492103=completed output/cram/nanopore_duo/.nxf.log
cram/nanopore | PASSED | 492104=completed output/cram/nanopore/.nxf.log
cram/single | PASSED | 492105=completed output/cram/single/.nxf.log
cram/trio | PASSED | 492106=completed output/cram/trio/.nxf.log