b197e1670a076b65838fd91b869a4ec1c3096c0f max Wed Sep 23 16:08:08 2026 -0700 Add Panmask Difficult 151b, the inverse of Panmask Easy 151b, for the Problematic Regions RTS Panmask marks easy regions under a "Problematic Regions" container, which Anna flagged as confusing. Rather than change the released Panmask Easy track, add a second track with the complement regions, built with featureBits (excluding assembly gaps and restricted to the 24 chromosomes Panmask itself covers). Checked the source first: Zenodo record 16755940 is still v1.4, same version already in use, MD5 verified. New track is alpha only for QA to pick up. refs #38375 diff --git src/hg/makeDb/trackDb/human/hg38/problematic.ra src/hg/makeDb/trackDb/human/hg38/problematic.ra index e538ab528dc..b1b0b2a5444 100644 --- src/hg/makeDb/trackDb/human/hg38/problematic.ra +++ src/hg/makeDb/trackDb/human/hg38/problematic.ra @@ -1,197 +1,208 @@ track problematicSuper shortLabel Problematic Regions longLabel Problematic/special genomic regions for sequencing or very variable regions superTrack on show html problematic group map track problematic parent problematicSuper shortLabel Problematic Regions longLabel Problematic/special genomic regions for sequencing or very variable regions compositeTrack on hideEmptySubtracks on visibility pack priority 1 type bigBed 3 + track comments shortLabel UCSC Unusual Regions longLabel UCSC unusual regions on assembly structure (manually annotated) type bigBed 9 + bigDataUrl /gbdb/hg38/problematic/comments.bb parent problematic priority 1 mouseOverField note searchIndex name searchTrix /gbdb/hg38/problematic/notes.ix noScoreFilter on track encBlacklist shortLabel ENCODE Blacklist V2 longLabel ENCODE Blacklist V2 type bigBed 4 bigDataUrl /gbdb/hg38/problematic/encBlacklist.bb parent problematic off priority 2 track grcExclusions shortLabel GRC Exclusions longLabel GRC Exclusion list: contaminations or false duplications type bigBed 4 bigDataUrl /gbdb/hg38/problematic/grcExclusions.bb parent problematic off priority 3 track highlyReproducible parent problematicSuper subGroup1 view Views beds=Regions vcfs=Variants compositeTrack on shortLabel Highly Reproducible Regions longLabel Highly Reproducible genomic regions for sequencing visibility hide html problematic priority 2 type bed 3 track highReproBeds parent highlyReproducible shortLabel Highly Reproducible Regions longLabel Highly Reproducible Regions type bigBed 9 + view beds visibility dense track highReproRegions parent highReproBeds bigDataUrl /gbdb/hg38/problematic/highRepro/highRepro.bb subGroups view=beds shortLabel Highly Reproducible Regions longLabel Highly Reproducible Regions type bigBed 9 + filterValues.sampleNames CQ-56,CQ-7,CQ-8,HR_NA10835,HR_NA12248,HR_NA12249,HR_NA12878 filterType.sampleNames multipleListOr track highReproVcfs parent highlyReproducible shortLabel Highly Reproducible Variants longLabel Highly Reproducible Variants hideEmptySubtracks on type vcfTabix view vcfs visibility hide track cq56Vcf parent highReproVcfs bigDataUrl /gbdb/hg38/problematic/highRepro/CQ-56.sort.vcf.gz subGroups view=vcfs shortLabel CQ-56 Variants longLabel CQ-56 Variants type vcfTabix track cq7Vcf parent highReproVcfs bigDataUrl /gbdb/hg38/problematic/highRepro/CQ-7.sort.vcf.gz subGroups view=vcfs shortLabel CQ-7 Variants longLabel CQ-7 Variants type vcfTabix track cq8Vcf parent highReproVcfs bigDataUrl /gbdb/hg38/problematic/highRepro/CQ-8.sort.vcf.gz subGroups view=vcfs shortLabel CQ-8 Variants longLabel CQ-8 Variants type vcfTabix track hr_na10835Vcf parent highReproVcfs bigDataUrl /gbdb/hg38/problematic/highRepro/HR_NA10835.sort.vcf.gz subGroups view=vcfs shortLabel HR_NA10835 Variants longLabel HR_NA10835 Variants type vcfTabix track hr_na12248Vcf parent highReproVcfs bigDataUrl /gbdb/hg38/problematic/highRepro/HR_NA12248.sort.vcf.gz subGroups view=vcfs shortLabel HR_NA12248 Variants longLabel HR_NA12248 Variants type vcfTabix track hr_na12249Vcf parent highReproVcfs bigDataUrl /gbdb/hg38/problematic/highRepro/HR_NA12249.sort.vcf.gz subGroups view=vcfs shortLabel HR_NA12249 Variants longLabel HR_NA12249 Variants type vcfTabix track hr_na12878Vcf parent highReproVcfs bigDataUrl /gbdb/hg38/problematic/highRepro/HR_NA12878.sort.vcf.gz subGroups view=vcfs shortLabel HR_NA12878 Variants longLabel HR_NA12878 Variants type vcfTabix track problematicGIAB parent problematicSuper compositeTrack on type bigBed 3 shortLabel GIAB Problematic Regions longLabel Difficult regions from GIAB via NCBI hideEmptySubtracks off visibility hide priority 3 html problematic track alldifficultregions parent problematicGIAB on bigDataUrl /gbdb/hg38/problematic/GIAB/alldifficultregions.bb shortLabel All difficult regions longLabel Genome In a Bottle: all difficult regions type bigBed 3 visibility dense track alllowmapandsegdupregions parent problematicGIAB on bigDataUrl /gbdb/hg38/problematic/GIAB/alllowmapandsegdupregions.bb shortLabel LowMap+SegDup longLabel Genome In a Bottle: lowMap+SegDup regions type bigBed 3 visibility dense track notinalldifficultregions parent problematicGIAB on bigDataUrl /gbdb/hg38/problematic/GIAB/notinalldifficultregions.bb shortLabel Not difficult regions longLabel Genome In a Bottle: not difficult regions type bigBed 3 visibility dense track notinalllowmapandsegdupregions parent problematicGIAB on bigDataUrl /gbdb/hg38/problematic/GIAB/notinalllowmapandsegdupregions.bb shortLabel Not lowMap+SegDup longLabel Genome In a Bottle: not lowMap+SegDup mapping regions type bigBed 3 visibility dense track panmask151b parent problematicSuper on bigDataUrl /gbdb/hg38/problematic/hg38.pm151b-v3.easy.bb shortLabel Panmask Easy 151b longLabel Panmask Easy 151b Regions: High accuracy for variant calling type bigBed 3 dataVersion pm151b-v3.easy.bed.gz (Panmask v1.4, Aug 6 2025, MD5: 2f59a43dab0b463bafcf3b59fc62) visibility hide html problematic + track panmask151bDifficult + parent problematicSuper on + release alpha + bigDataUrl /gbdb/hg38/problematic/hg38.pm151b-v3.notEasy.bb + shortLabel Panmask Difficult 151b + longLabel Panmask Difficult 151b Regions: Lower accuracy for variant calling, inverse of Panmask Easy + type bigBed 3 + dataVersion Inverse of pm151b-v3.easy.bed.gz (Panmask v1.4, Aug 6 2025), computed with featureBits + visibility hide + html problematic + searchTable comments searchPriority 0.5 searchType bigBed searchDescription Special genome loci: gene clusters, haplotypes, patches, etc.