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/doc/hg38/problematic.txt src/hg/makeDb/doc/hg38/problematic.txt index 55626aefea9..78730657ba0 100644 --- src/hg/makeDb/doc/hg38/problematic.txt +++ src/hg/makeDb/doc/hg38/problematic.txt @@ -1,130 +1,153 @@ cd /hive/data/genomes/hg38/bed/problematic/ # note that the hg19 directory is /hive/data/genomes/hg19/bed/specialRegions/, the track name used to be different # add the ENCODE blacklist wget 'https://github.com/Boyle-Lab/Blacklist/blob/master/lists/hg38-blacklist.v2.bed.gz?raw=true' -O hg38-blacklist.v2.bed.gz gunzip hg38-blacklist.v2.bed.gz mkdir bb bedSort hg38-blacklist.v2.bed hg38-blacklist.v2.bed bedToBigBed hg38-blacklist.v2.bed /hive/data/genomes/hg38/chrom.sizes bb/encBlacklist.bb -type=bed4 -tab # bring over the manual comments track, mostly manual work cd ../manualComments ln -s ../../../../hg19/bed/specialRegions/manualComments mv manualComments hg19Comments cat hg19Comments/manual.bed | cut -f1-4 > hg19.bed ~/bin/x86_64/liftOver -tab hg19.bed /hive/data/genomes/hg19/bed/liftOver/hg19ToHg38.over.chain.gz manual.lift.bed unmapped.lift.bed # -- manual step! -- fixed up manual.lift.bed manually adding PAR regions cat hg19Comments/manual.bed | cut -f4- | sort > annots.tsv tabJoin annots.tsv 0 manual.lift.bed 3 > manual.bed # -- manual step -- fixed up manual.bed hgsql hg38 -e 'select * from chromInfo' | grep chrUn | cut -f-2 |tawk '{$3=$2; $2=0; $4="unplaced"; $5="ChrUn contains clone contigs that cannot be confidently placed on a specific chromosome."; $6="none"; print}' > chrUn.bed # fixes hgsql hg38 -e 'select * from chromInfo' | grep _fix | cut -f-2 |tawk '{$3=$2; $2=0; $4="fix"; $5="The chr_fix chromosomes, such as chr1_KN538361v1_fix, are fix patches currently available for the hg19 and hg38 assemblies that represent changes to the existing sequence. These are generally error corrections (such as base changes, component replacements/updates, switch point updates or tiling path changes) or assembly improvements (such as extension of sequence into gaps). These fix patch scaffold sequences are given chromosome context through alignments to the corresponding chromosome regions, in the \"Mapping and Sequencing > GRC Patch Release\" track. See also <a href=\"https://genome.ucsc.edu/FAQ/FAQdownloads#downloadFix\" target=_blank>the FAQ</a> for more information."; $6="none"; print}' > chrFix.bed # alts hgsql hg38 -e 'select * from chromInfo' | grep alt | cut -f-2 |tawk '{$3=$2; $2=0; $4="alt"; $5="The chr_alt chromosomes, such as chr5_KI270794v1_alt, are alternative sequences that differ from the reference genome currently available for a few assemblies including danRer11, hg19, and hg38. These are regions of the genome that exhibit sufficient variability to prevent adequate representation by a single sequence. UCSC labels these haplotype sequences by appending "_alt" to their names. These alternative loci scaffolds (such as KI270794.1 in the hg38 assembly, referenced as chr5_KI270794v1_alt in the browser), are mapped to the genome and provide suppemental genomic information on these variable locations. To find the regions these alternate sequences correspond to in the genome you may use the Alt Haplotypes track if one is available. See also <a href=\"https://genome.ucsc.edu/FAQ/FAQdownloads#downloadAlt\" target=_blank>the FAQ</a> for more information."; $6="none"; print}' > chrAlt.bed # various other gene clusters bigBedToBed /gbdb/hg38/ncbiRefSeq/ncbiRefSeqOther.bb stdout | less | grep -v pseudo | grep -v "T cell" -i | grep -v tRNA | grep -v immuno | grep -v constant | grep -v miR | grep -v UGT1A | grep -v PCDHA | grep -v PCDHB | cut -f1-4,18 | tawk '{$5=$5" HGNC ID:"$4" This is a cluster of many very similar genes based on the <b>Genes and Gene Predictions > NCBI RefSeq > RefSeq Other</b> Track"; $4="cluster"; print}' > chrClusters.bed # put everything together and make trix files cat manual.bed chr*.bed | sort -k1,1 -k2,2n | tawk '{desc=$5; desc2=$6; $5="0"; $6="+"; $7=$2; $8=$3; $9="0,0,0"; $10=desc; $11=desc2; print}' > all.bed bedToBigBed all.bed /hive/data/genomes/hg38/chrom.sizes comments.bb -tab -as=manual.as -type=bed9+ -extraIndex=name cut -f4,10 all.bed > notes.txt ixIxx notes.txt notes.ix notes.ixx # Tue Apr 11 02:12:18 PDT 2023 # add the GRC exclude list, from MarkD cat ~markd/public_html/browser/grc-bad/GCA_000001405.15_GRCh38_GRC_exclusions.bed | grep -v description > grcExclusions.bed bedSort grcExclusions.bed grcExclusions.bed bedToBigBed grcExclusions.bed ../../chrom.sizes bb/grcExclusions.bb -tab -type=bed4 # Add highly reproducible regions (#31122): # https://zenodo.org/record/5275189#.ZEhKRezMI-S cd /hive/data/genomes/hg38/bed/problematic/ mkdir highRepro # The zenodo link has a bunch of links with "?download=1" on the url, copy and paste them # into a text file to remove that and then download them vim urls.txt wget --quiet --input-file=urls.txt # all of the beds are just bed3's head *.bed ==> CQ-56.bed <== chr1 12857 12904 chr1 12932 13028 chr1 13129 13367 chr1 13520 13633 ... # so turn those into bigBeds and link everything to /gbdb for f in $(ls *.bed); do base=$(basename -s .bed $f); bedSort ${f} ${f}.sorted; bedToBigBed ${f}.sorted../../../chrom.sizes ${base}.bb; done # for some reason tabix doesn't like to be run in a for loop from ls, needs find for f in $(find . -name "*.vcf.gz"); do tabix --verbosity 3 -p vcf "${f}"; done mkdir -p /gbdb/hg38/problematic/highRepro ln -s `pwd`/*.bb /gbdb/hg38/problematic/highRepro/ ln -s `pwd`/*.vcf.gz* /gbdb/hg38/problematic/highRepro/ # turns the beds into one single bed with the overlapped regions: for f in $(ls *.bed); do echo $f; n=${f/.bed/}; tawk -v name=${n} '{print $0,name}' $f > ${n}.bed4; done cat *.bed4 | sort -k1,1 -k2,2n > highRepro.allRegions bedOverlapMerge highRepro.allRegions | tawk '{print $0,0,".",$2,$2,"0,0,0",gensub(/\//, ",", "g",$4)}' > highRepro.merged bedToBigBed -type=bed9+1 -tab -as=highRepro.as highRepro.merged ../../../chrom.sizes highRepro.bb ############################################################################# # problematicGIAB: Difficult regions from GIAB via NCBI - Megna/Gerardo # Redmine #34253 # Megna workflow for v3.3: cp /cluster/home/mchalama/public_html/tracks/CoLoRSdb/genomes.txt /cluster/home/mchalama/public_html/tracks/difficult cp /cluster/home/mchalama/public_html/tracks/CoLoRSdb/hub.txt /cluster/home/mchalama/public_html/tracks/difficult cp /cluster/home/mchalama/public_html/tracks/CoLoRSdb/hg38/CoLoRSdb.html /cluster/home/mchalama/public_html/tracks/difficult cp /cluster/home/mchalama/public_html/tracks/CoLoRSdb/hg38/trackDb.txt /cluster/home/mchalama/public_html/tracks/difficult mkdir hg38 mv /cluster/home/mchalama/public_html/tracks/difficult/CoLoRSdb.html /cluster/home/mchalama/public_html/tracks/difficult/hg38 mv /cluster/home/mchalama/public_html/tracks/difficult/trackDb.txt /cluster/home/mchalama/public_html/tracks/difficult/hg38 edit genomes.txt edit hub.txt; got contact of PI from here: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.3/README.md wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.3/GRCh38@all/Union/GRCh38_alldifficultregions.bed.gz wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.3/GRCh38@all/Union/GRCh38_alllowmapandsegdupregions.bed.gz wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.3/GRCh38@all/Union/GRCh38_notinalldifficultregions.bed.gz wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.3/GRCh38@all/Union/GRCh38_notinalllowmapandsegdupregions.bed.gz #edit trackDb.txt to include the 4 datasets #Bed to BigBed conversion because I realized you can't see beds properly on the hub bedToBigBed /cluster/home/mchalama/public_html/tracks/difficult/hg38/GRCh38_alldifficultregions.bed.gz /cluster/home/mchalama/public_html/tracks/difficult/hg38.chrom.sizes GRCh38_alldifficultregions.bb bedToBigBed /cluster/home/mchalama/public_html/tracks/difficult/hg38/GRCh38_alllowmapandsegdupregions.bed.gz /cluster/home/mchalama/public_html/tracks/difficult/hg38.chrom.sizes GRCh38_alllowmapandsegdupregions.bb bedToBigBed /cluster/home/mchalama/public_html/tracks/difficult/hg38/GRCh38_notinalldifficultregions.bed.gz /cluster/home/mchalama/public_html/tracks/difficult/hg38.chrom.sizes GRCh38_notinalldifficultregions.bb bedToBigBed /cluster/home/mchalama/public_html/tracks/difficult/hg38/GRCh38_notinalllowmapandsegdupregions.bed.gz /cluster/home/mchalama/public_html/tracks/difficult/hg38.chrom.sizes GRCh38_notinalllowmapandsegdupregions.bb edit the html file to include information about the track #open genome browser #navigate to custom hub and paste the following URL #https://hgwdev.gi.ucsc.edu/~mchalama/tracks/difficult/hub.txt # Gerardo workflow for v3.5: # Copied the trackDb.txt into the human/hg38/problematic.ra and copied html description into problematic html # Downloaded the v3.5 data cd /hive/data/genomes/hg38/bed/ mkdir problematic; cd problematic mkdir GIAB; cd GIAB wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/GRCh38@all/Union/GRCh38_alldifficultregions.bb wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/GRCh38@all/Union/GRCh38_alllowmapandsegdupregions.bb wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/GRCh38@all/Union/GRCh38_notinalldifficultregions.bb wget https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/genome-stratifications/v3.5/GRCh38@all/Union/GRCh38_notinalllowmapandsegdupregions.bb cd /gbdb/hg38/ mkdir problematic; cd problematic mkdir GIAB; cd GIAB # Made symlinks ln -s /hive/data/genomes/hg38/bed/problematic/GIAB/alldifficultregions.bb ln -s /hive/data/genomes/hg38/bed/problematic/GIAB/notinalldifficultregions.bb ln -s /hive/data/genomes/hg38/bed/problematic/GIAB/alllowmapandsegdupregions.bb ln -s /hive/data/genomes/hg38/bed/problematic/GIAB/notinalllowmapandsegdupregions.bb # Updated the bigDataUrl problematic.ra and problematic.html ############################################################################# # Panmask track, Max, Aug 29 2025 wget https://zenodo.org/records/16755940/files/hg38.pm151b-v3.easy.bed.gz?download=1 mv hg38.pm151b-v3.easy.bed.gz\?download\=1 hg38.pm151b-v3.easy.bed.gz bedToBigBed hg38.pm151b-v3.easy.bed.gz ../../../chrom.sizes hg38.pm151b-v3.easy.bb + +# Panmask Difficult track: inverse of Panmask Easy, Claude for Max, Sep 22 2026, refs #38375 +# Anna pointed out that a track called "Panmask" under a "Problematic Regions" container is +# confusing, since it marks the easy regions, not the problematic ones. Rather than changing +# the released Panmask Easy track, we add a second track with the inverse regions, for use in +# the Problematic Regions Recommended Track Set. Checked the source first: Zenodo record +# 16755940 is still at v1.4 (Aug 6 2025, finalized Sep 22 2025), same version already in use, +# and the local file's MD5 matches the file on Zenodo, so no re-download was needed. +cd /hive/data/genomes/hg38/bed/problematic/panmask +# Panmask covers only the 24 main chromosomes (no chrM, no alts/randoms/fixes), so restrict +# the complement to that same set rather than the full 711-sequence chrom.sizes, and exclude +# assembly gaps from the complement with the !gap idiom, so centromeric N-runs don't get +# double-counted as "hard" on top of the existing Gap track. +awk '$1 !~ /_/ && $1 != "chrM" {printf "%s\t%s\thg38.2bit\n", $1, $2}' \ + ../../../chrom.sizes > primary24.chrom.sizes +featureBits hg38 '!/gbdb/hg38/problematic/hg38.pm151b-v3.easy.bb' '!gap' \ + -chromSize=primary24.chrom.sizes -bed=hg38.pm151b-v3.notEasy.bed -minSize=1 +# 359,192,609 bases of 2,937,659,104 (12.227%) -- the complement of Panmask Easy's 87.8% +bedSort hg38.pm151b-v3.notEasy.bed hg38.pm151b-v3.notEasy.bed +cut -f1-3 hg38.pm151b-v3.notEasy.bed > hg38.pm151b-v3.notEasy.bed3 +bedToBigBed hg38.pm151b-v3.notEasy.bed3 ../../../chrom.sizes hg38.pm151b-v3.notEasy.bb -type=bed3 -tab +gzip -k hg38.pm151b-v3.notEasy.bed3 +mv hg38.pm151b-v3.notEasy.bed3.gz hg38.pm151b-v3.notEasy.bed.gz