8a5a466f5e13a020954014cdefc81400072db516 max Tue Apr 21 08:29:55 2026 -0700 lrSv: add hprc2 hs1 subtrack using T2T-CHM13 wave VCF, refs #36258 The HPRC release-2 pangenome publishes a wave-decomposed VCF against both GRCh38 and T2T-CHM13. We already had the GRCh38 version as the hprc2Sv subtrack on hg38; this adds the parallel T2T-CHM13 build under /gbdb/hs1/lrSv/hprc2.bb. The existing trackDb stanza (bigDataUrl /gbdb/$D/lrSv/hprc2.bb) picks it up on hs1 without changes. 1,451,269 SV rows kept (937,425 INS, 360,960 DEL, 147,898 COMPLEX, 4,986 INV) using the existing lrSvHprc2VcfToBed.py converter. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/doc/hg38/lrSv.txt src/hg/makeDb/doc/hg38/lrSv.txt index b164679d86d..918b750b12e 100644 --- src/hg/makeDb/doc/hg38/lrSv.txt +++ src/hg/makeDb/doc/hg38/lrSv.txt @@ -1,434 +1,437 @@ # 2026-03-25 Claude max # Long-read structural variants supertrack # First subtrack: Han 945 - SVs from 945 Han Chinese individuals # Paper: Gong et al. 2025, Nat Commun, PMID 39929826 # Data: OMIX repository, NGDC # Download VCF mkdir -p /hive/data/genomes/hg38/bed/lrSv/han945 cd /hive/data/genomes/hg38/bed/lrSv/han945 # VCF was downloaded from OMIX (accession OED00945268) # File: OED00945268_Han_945samples_SV.vcf.gz # 111,288 SVs: 49,518 DEL, 42,300 INS, 13,503 DUP, 5,595 INV, 372 TRA # Site-only VCF (no per-sample genotypes), merged with SURVIVOR v1.0.6 # Convert VCF to BED and build bigBed python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvVcfToBed.py \ OED00945268_Han_945samples_SV.vcf.gz han945.bed bedSort han945.bed han945.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSv.as \ -tab han945.sorted.bed /hive/data/genomes/hg38/chrom.sizes han945.bb # Symlink mkdir -p /gbdb/hg38/lrSv ln -sf /hive/data/genomes/hg38/bed/lrSv/han945/han945.bb /gbdb/hg38/lrSv/han945.bb # Convert SUPP_VEC to per-sample genotype VCF for vcfTabix display python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvHan945SuppVecToVcf.py \ OED00945268_Han_945samples_SV.vcf.gz han945genotypes.vcf bcftools sort han945genotypes.vcf -Oz -o han945genotypes.sorted.vcf.gz tabix -p vcf han945genotypes.sorted.vcf.gz ########## # 2026-03-26 Claude max # Second subtrack: 1KG ONT - SVs from 1,019 diverse humans (1000 Genomes ONT) # Paper: Schloissnig et al. 2025, Nature, PMID 40702182 # Data: 1000 Genomes ONT Vienna, IGSR/EBI FTP mkdir -p /hive/data/genomes/hg38/bed/lrSv/1k-1019 cd /hive/data/genomes/hg38/bed/lrSv/1k-1019 # VCF downloaded from: # https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1KG_ONT_VIENNA/release/v1.1/svan-annotation/ # File: final-vcf.unphased.SVAN_1.3.vcf.gz # 161,332 SVAN-annotated SVs: 75,324 INS, 66,192 DEL, 19,816 COMPLEX # Site-only VCF (no genotypes), SVAN v1.3 annotations # Called with SAGA framework against pangenome graph # NOTE: VCF contig sizes match hs1 (CHM13/T2T), not hg38. # bigGuessDb confirms hs1. So we build a native hs1 bigBed and liftOver to hg38. # Convert SVAN VCF to BED, adding allele counts from the phased VCF. # The phased VCF (shapeit5) has AC/AN/AF for 164,625 variants. # Of the 161,332 SVAN variants, 158,469 (98.2%) have a matching phased variant. # The 2,863 unmatched SVs get alleleCount=-1 (displayed as "Unknown"). # Fields kept from SVAN: svClass, svLen, insType, family, percResolved, tsdLen, # polyaLen, conformation, rtLen, nbMotifs, srcGene, nbExons, notCanonical. # Dropped: SOURCE_COORD (0% populated), all *_SEQ fields, *_MAPQ, REPEAT_BKP, # DUP_COORD, MOTIFS, CONFORMATION_EXT, HEXAMER_*, *_TD/TEMP_COORD (all rare/long). python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSv1kgOntVcfToBed.py \ final-vcf.unphased.SVAN_1.3.vcf.gz 1kgOnt.hs1.bed \ /hive/data/genomes/hs1/chrom.sizes \ shapeit5-phased-callset_final-vcf.phased.vcf.gz # 161,332 records, 158,469 with allele counts # Build hs1 bigBed bedSort 1kgOnt.hs1.bed 1kgOnt.hs1.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSv1kgOnt.as \ -tab 1kgOnt.hs1.sorted.bed /hive/data/genomes/hs1/chrom.sizes 1kgOnt.hs1.bb # LiftOver to hg38 liftOver -tab -bedPlus=9 1kgOnt.hs1.bed \ /gbdb/hs1/liftOver/hs1ToHg38.over.chain.gz \ 1kgOnt.hg38.bed 1kgOnt.unmapped.bed # 148,375 mapped, ~13K unmapped # Build hg38 bigBed bedSort 1kgOnt.hg38.bed 1kgOnt.hg38.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSv1kgOnt.as \ -tab 1kgOnt.hg38.sorted.bed /hive/data/genomes/hg38/chrom.sizes 1kgOnt.hg38.bb # Symlinks for both assemblies mkdir -p /gbdb/hg38/lrSv /gbdb/hs1/lrSv ln -sf /hive/data/genomes/hg38/bed/lrSv/1k-1019/1kgOnt.hg38.bb /gbdb/hg38/lrSv/1kgOnt.bb ln -sf /hive/data/genomes/hg38/bed/lrSv/1k-1019/1kgOnt.hs1.bb /gbdb/hs1/lrSv/1kgOnt.bb ########## # 2026-03-26 Claude max # Third subtrack: ToMMo Japanese SVs - 333 individuals (111 trios) # Paper: Otsuki et al. 2022, Commun Biol, PMID 36127505 # Data: jMorp portal, ToMMo mkdir -p /hive/data/genomes/hg38/bed/lrSv/tommoJp cd /hive/data/genomes/hg38/bed/lrSv/tommoJp # VCF downloaded from jMorp: # https://jmorp.megabank.tohoku.ac.jp/datasets/tommo-jsv1-20211208-af # File: tommo-JSV1-20211208-GRCh38-without-genotype-count.vcf.gz # 74,201 SVs: 37,981 DEL, 36,220 INS # Site-only VCF, merged with SURVIVOR v1.0.6 # Native GRCh38 coordinates (confirmed via contig headers) # Trio-based: 111 families, includes Mendelian error rates # Convert VCF to BED and build bigBed python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvTommoJpVcfToBed.py \ tommo-JSV1-20211208-GRCh38-without-genotype-count.vcf.gz tommoJp.bed bedSort tommoJp.bed tommoJp.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvTommoJp.as \ -tab tommoJp.sorted.bed /hive/data/genomes/hg38/chrom.sizes tommoJp.bb ########## # 2026-03-26 Claude max # Fourth subtrack: AoU 1K - SVs from 1,027 AoU individuals (PacBio HiFi) # Paper: Garimella et al. 2025, medRxiv, PMID 41256123 # Data: Supplementary media-2 from preprint mkdir -p /hive/data/genomes/hg38/bed/lrSv/aou1k cd /hive/data/genomes/hg38/bed/lrSv/aou1k # Downloaded supplementary CSV from preprint (media-2.gz) # 541,049 SVs: 444,524 INS, 96,525 DEL (autosomes only) # Population-specific AFs (AFR, AMR, EAS, EUR, SAS) # Gene annotations (OMIM, disease, cancer, ACMG), regulatory elements # eQTL, GWAS, and SV-trait associations # Native GRCh38 coordinates # Convert CSV to BED and build bigBed python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvAou1kCsvToBed.py media-2.gz aou1k.bed bedSort aou1k.bed aou1k.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvAou1k.as \ -tab aou1k.sorted.bed /hive/data/genomes/hg38/chrom.sizes aou1k.bb ########## # 2026-04-16 Claude max # Fifth subtrack: Genomic Answers for Kids (GA4K) - Children's Mercy # PacBio HiFi long-read SVs. 502-sample site-only release. # Primary reference for the program: Cohen et al. 2022, Genet Med, PMID 35305867 # Data release: https://github.com/ChildrensMercyResearchInstitute/GA4K # (The matched GA4K small-variant release is handled in the Variant # Frequencies collection; see ~/kent/src/hg/makeDb/doc/hg38/varFreqs.txt.) mkdir -p /hive/data/genomes/hg38/bed/lrSv/GA4K cd /hive/data/genomes/hg38/bed/lrSv/GA4K # Data cloned from the ChildrensMercyResearchInstitute/GA4K GitHub repo. # pacbio_sv_vcf/pb_joint_merged.sv.vcf.gz: # 115,554 replicated SVs from 502 samples (52,564 DEL, 58,219 INS, # 4,408 DUP, 363 INV). Jasmine v1.1.4 merge, filtered to SVs observed in # 2+ unrelated GA4K individuals or matching a Decode/HPRC SV (svpack match). python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvGa4kSvVcfToBed.py \ pacbio_sv_vcf/pb_joint_merged.sv.vcf.gz ga4kSv.bed bedSort ga4kSv.bed ga4kSv.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvGa4kSv.as \ -tab ga4kSv.sorted.bed /hive/data/genomes/hg38/chrom.sizes ga4kSv.bb ########## # 2026-04-17 Claude max # Sixth subtrack: deCODE Icelandic high-confidence long-read SVs. # Paper: Beyter et al. 2021, Nat Genet, PMID 33972781 # Data: https://github.com/DecodeGenetics/LRS_SV_sets mkdir -p /hive/data/genomes/hg38/bed/lrSv/decode cd /hive/data/genomes/hg38/bed/lrSv/decode # Downloaded from the DecodeGenetics/LRS_SV_sets GitHub repo: # ont_sv_high_confidence_SVs.sorted.vcf.gz (+ .tbi) # ont_sv_high_confidence_tandemdup.csv (auxiliary tandem-duplication # annotations; not currently displayed as a browser track) # 133,886 high-confidence SVs: 55,649 DEL, 75,050 INS, 3,187 INSDEL. # Site-only, native GRCh38 coordinates. INFO fields: SVTYPE, END, SVLEN, # TRRBEGIN, TRREND (surrounding tandem-repeat region). python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvDecodeVcfToBed.py \ ont_sv_high_confidence_SVs.sorted.vcf.gz decodeSv.bed bedSort decodeSv.bed decodeSv.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvDecode.as \ -tab decodeSv.sorted.bed /hive/data/genomes/hg38/chrom.sizes decodeSv.bb ########## # 2026-04-17 Claude max # Seventh subtrack: HGSVC3 - Human Genome Structural Variation Consortium # phase 3. 65 diverse samples, PacBio HiFi + ONT, PAV-based SV discovery. # Paper: Logsdon et al. 2025, Nature, PMID 40702183 # Data: IGSR FTP release v1.0 (annotation_table/) mkdir -p /hive/data/genomes/hg38/bed/lrSv/hgsvc3 cd /hive/data/genomes/hg38/bed/lrSv/hgsvc3 # Downloaded the two SV annotation tables from: # https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC3/release/Variant_Calls/1.0/GRCh38/annotation_table/ # variants_GRCh38_sv_insdel_HGSVC2024v1.0.tsv.gz (176,232 DEL+INS) # variants_GRCh38_sv_inv_HGSVC2024v1.0.tsv.gz (300 INV) # The two tables are complementary: the insdel table holds all # insertions+deletions (with HOM_REF/HOM_TIG/TE columns specific to # insertions+deletions), while the inv table holds inversions (with an # RGN_REF_INNER column describing the inner inverted region). The lrSv # subtrack merges them into a single bigBed. python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvHgsvc3TsvToBed.py \ variants_GRCh38_sv_insdel_HGSVC2024v1.0.tsv.gz \ variants_GRCh38_sv_inv_HGSVC2024v1.0.tsv.gz \ hgsvc3.bed bedSort hgsvc3.bed hgsvc3.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvHgsvc3.as \ -tab hgsvc3.sorted.bed /hive/data/genomes/hg38/chrom.sizes hgsvc3.bb # The same process is applied natively to T2T-CHM13 (hs1) using the HGSVC3 # T2T-CHM13 annotation tables. See ~/kent/src/hg/makeDb/doc/hs1/lrSv.txt. ########## # 2026-04-17 Claude max # Eighth subtrack: Kim et al. 2026 - PacBio HiFi long-read SVs from 100 # post-mortem brain samples (Parkinson's disease / ILBD / healthy controls). # Paper: Kim et al. 2026, bioRxiv, PMID 41929179 # Data: Supplementary Table 13 (media-13.txt) from the preprint. mkdir -p /hive/data/genomes/hg38/bed/lrSv/kwanho2026 cd /hive/data/genomes/hg38/bed/lrSv/kwanho2026 # media-13.txt holds the final high-confidence catalog of 74,552 SVs # (34,056 INS, 29,545 DEL, 9,707 DUP, 1,244 INV) across three cohorts # (PD: 35, ILBD: 31, HC: 34; 100 samples total). paper.txt has the preprint # text for reference. Numeric fields use comma thousands-separators inside # quoted strings, so the converter parses the TSV with the csv module. python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvKwanhoTsvToBed.py \ media-13.txt kwanho.bed bedSort kwanho.bed kwanho.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvKwanho.as \ -tab kwanho.sorted.bed /hive/data/genomes/hg38/chrom.sizes kwanho.bb ########## # 2026-04-17 Claude max # Ninth subtrack: GWAS SVatalog - 101 long-read whole-genome sequences # from SickKids (Chirmade et al. 2026, Heredity, PMID 41203876). # Data: zenodo.org/records/13367574 (sv_annotations.tsv) mkdir -p /hive/data/genomes/hg38/bed/lrSv/shirmade101 cd /hive/data/genomes/hg38/bed/lrSv/shirmade101 # sv_annotations.tsv holds 87,183 SVs (del, ins, dup, inv, complex) from 101 # long-read WGS samples, annotated with gene overlaps, ClinGen / gnomAD # constraints, OMIM / ClinVar / DGV / Decipher regional overlaps. # Coordinates in the source TSV are 1-based closed; the converter shifts to # standard 0-based half-open BED. python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvChirmade101TsvToBed.py \ sv_annotations.tsv chirmade101.bed bedSort chirmade101.bed chirmade101.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvChirmade101.as \ -tab chirmade101.sorted.bed /hive/data/genomes/hg38/chrom.sizes chirmade101.bb ########## # 2026-04-20 Claude max # Tenth subtrack: Gustafson et al. 2024 - 100 1000 Genomes ONT samples # Paper: Gustafson et al. 2024, Genome Res, PMID 39358015 # Data: 1000g-ont S3 bucket (Jasmine-merged site-level SV VCF) # Note: distinct cohort from the Schloissnig "Vienna" 1KG-ONT track (lrSv1kgOnt) mkdir -p /hive/data/genomes/hg38/bed/lrSv/gustafson cd /hive/data/genomes/hg38/bed/lrSv/gustafson wget https://s3.amazonaws.com/1000g-ont/Gustafson_etal_2024_preprint_SUPPLEMENTAL/20240423_jasmine_intrasample_noBND_custom_suppvec_alphanumeric_header_JASMINE.vcf.gz wget https://s3.amazonaws.com/1000g-ont/Gustafson_etal_2024_preprint_SUPPLEMENTAL/20240423_jasmine_intrasample_noBND_custom_suppvec_alphanumeric_header_JASMINE.vcf.gz.csi # 113,696 SVs across 100 samples (500 sample-caller columns total; each sample # contributes up to 5 per-caller entries via Sniffles2/cuteSV/SVIM on minimap2 # alignments plus hapdiff on Flye and Shasta assemblies). Site-only BED from # INFO fields: SVTYPE, END, SVLEN, SUPP, VARCALLS, PRECISE, STRANDS. The # converter clips END on chrM to the chromosome length (source file has one # chrM DUP with END=16570 vs. chrM length 16569). python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvGustafsonVcfToBed.py \ 20240423_jasmine_intrasample_noBND_custom_suppvec_alphanumeric_header_JASMINE.vcf.gz \ gustafson.bed bedSort gustafson.bed gustafson.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvGustafson.as \ -tab gustafson.sorted.bed /hive/data/genomes/hg38/chrom.sizes gustafson.bb ########## # 2026-04-20 Claude max # Eleventh subtrack: HGSVC2 - phase 2 of the Human Genome Structural # Variation Consortium, 32 haplotype-resolved genomes (5 superpopulations). # Paper: Ebert et al. 2021, Science, PMID 33632895 # Data: IGSR FTP (HGSVC2 v2.0 integrated callset freeze 4) mkdir -p /hive/data/genomes/hg38/bed/lrSv/hgsvc2 cd /hive/data/genomes/hg38/bed/lrSv/hgsvc2 wget https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/release/v2.0/integrated_callset/variants_freeze4_sv_insdel.tsv.gz wget https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/release/v2.0/integrated_callset/variants_freeze4_sv_inv.tsv.gz # Two annotation tables are complementary (same structure as HGSVC3): the # insdel table holds DEL + INS with POP_*_AF population allele frequencies # imputed back into the 1000 Genomes cohort; the inv table holds INV with # an RGN_REF_INNER column. The converter merges them into a single bigBed. python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvHgsvc2TsvToBed.py \ variants_freeze4_sv_insdel.tsv.gz \ variants_freeze4_sv_inv.tsv.gz \ hgsvc2.bed bedSort hgsvc2.bed hgsvc2.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvHgsvc2.as \ -tab hgsvc2.sorted.bed /hive/data/genomes/hg38/chrom.sizes hgsvc2.bb ########## # 2026-04-20 Claude max # Twelfth subtrack: 1000 Genomes 3,202-sample Illumina SHORT-READ GATK-SV # release. Included in the lrSv collection solely as a short-read # comparator; it is NOT a long-read dataset. # Paper: Byrska-Bishop et al. 2022, Cell, PMID 36055201 # Data: 1KGP_3202.gatksv_svtools_novelins.freeze_V3.wAF.vcf.gz (IGSR FTP) mkdir -p /hive/data/genomes/hg38/bed/lrSv/onekg3202sr cd /hive/data/genomes/hg38/bed/lrSv/onekg3202sr wget https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20210124.SV_Illumina_Integration/1KGP_3202.gatksv_svtools_novelins.freeze_V3.wAF.vcf.gz # 173,366 site-level SVs across 7 classes (DEL, INS, DUP, INV, CPX, CNV, # CTX) with AC/AN/AF and per-superpopulation AFs (AFR/AMR/ASN/EUR/SAN). # The converter extracts site-level INFO into bed9+, preserving the # FILTER column so users can see PASS vs LowQual / HWE / etc. python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSv1kg3202SrVcfToBed.py \ 1KGP_3202.gatksv_svtools_novelins.freeze_V3.wAF.vcf.gz onekg3202sr.bed bedSort onekg3202sr.bed onekg3202sr.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSv1kg3202Sr.as \ -tab onekg3202sr.sorted.bed /hive/data/genomes/hg38/chrom.sizes onekg3202sr.bb ########## # 2026-04-20 Claude max # Thirteenth subtrack: HPRC release-2 pangenome SVs (233 samples). # No peer-reviewed publication yet; see HPRC release page: # https://humanpangenome.org/hprc-data-release-2/ # Sample list (alignments v2.0): # https://github.com/human-pangenomics/hprc_intermediate_assembly/blob/main/data_tables/pangenomes/alignments_v2.0.csv mkdir -p /hive/data/genomes/hg38/bed/lrSv/hprc2 cd /hive/data/genomes/hg38/bed/lrSv/hprc2 # Pangenome graph (referenced in the doc html): wget https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/hprc-v2.0-mc-grch38.sv.gfa.gz # wave-decomposed VCF (what we actually convert): wget https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/hprc-v2.0-mc-grch38.wave.vcf.gz # The wave VCF contains ~20M atomic alleles including SNVs. The converter # streams the multi-allelic rows, explodes one BED row per ALT, and keeps # only SV-sized alleles (|LEN| >= 50 bp) plus all records carrying the # INV flag. 1,483,114 SVs kept (1,106,190 INS, 192,597 DEL, 178,178 # COMPLEX, 6,149 INV). python3 ~/kent/src/hg/makeDb/scripts/lrSv/lrSvHprc2VcfToBed.py \ hprc-v2.0-mc-grch38.wave.vcf.gz hprc2.bed bedSort hprc2.bed hprc2.sorted.bed bedToBigBed -type=bed9+ -as=$HOME/kent/src/hg/makeDb/scripts/lrSv/lrSvHprc2.as \ -tab hprc2.sorted.bed /hive/data/genomes/hg38/chrom.sizes hprc2.bb +# HPRC also releases a wave VCF against T2T-CHM13; the hs1 version of this +# subtrack is built in ~/kent/src/hg/makeDb/doc/hs1/lrSv.txt. + ########## # 2026-04-20 Claude max # CPC + HPRC Phase 1 pangenome SVs (105 samples). # Paper: Gao et al. 2023, Nature, PMID 37316654 # Data : https://github.com/Shuhua-Group/Chinese-Pangenome-Consortium-Phase-I # The VCF is on T2T-CHM13v2 (hs1) contigs renamed "CHM13v2.chrN". # Source VCF (CPC.HPRC.Phase1.processed.SVs.normed.vcf.gz, 3.7 GB) was # produced with pggb + vcfwave + bcftools norm; each graph snarl appears # as one VCF row per alternative allele, with genotypes for 105 samples. mkdir -p /hive/data/genomes/hg38/bed/lrSv/cpc1 cd /hive/data/genomes/hg38/bed/lrSv/cpc1 # (VCF already placed here by the user) # Run conversion + liftOver + bigBed for both hs1 (native) and hg38 (lifted). # The script strips the "CHM13v2." prefix, classifies each alt by length # delta with a 50 bp threshold (INS, DEL, CPX, or dropped), collapses all # alts of one snarl ID into a single row (MIXED when types disagree), # and writes 16-column bed rows with AC/AN/AF and NS. bash ~/kent/src/hg/makeDb/scripts/lrSv/lrSvCpc1Build.sh # hs1 bigBed: 97,205 sites (4.7 MB) # hg38 lifted: 81,261 sites (4.1 MB), 15,944 unmapped # Symlinks for both assemblies mkdir -p /gbdb/hs1/lrSv /gbdb/hg38/lrSv ln -sf /hive/data/genomes/hg38/bed/lrSv/cpc1/cpc1.hs1.bb /gbdb/hs1/lrSv/cpc1.bb ln -sf /hive/data/genomes/hg38/bed/lrSv/cpc1/cpc1.hg38.bb /gbdb/hg38/lrSv/cpc1.bb ########## # 2026-04-20 Claude max # Arabic Pangenome Reference (APR) SVs # Paper: Nassir et al. 2025, Nat Commun, PMID 40707445 # Data : https://www.mbru.ac.ae/the-arab-pangenome-reference/ # (SharePoint download page under APR Nuclear/Pangenome) # Source: apr_review_v1_2902_chm13.vcf.gz (1.5 GB, 21M variants, # contigs named chrN with CHM13v2 lengths, multi-allelic rows). mkdir -p /hive/data/genomes/hg38/bed/lrSv/apr cd /hive/data/genomes/hg38/bed/lrSv/apr # (VCF placed here by the user from the MBRU SharePoint download) # Run converter + liftOver + bigBed for both hs1 (native) and hg38 (lifted). # The script iterates the comma-separated ALT alleles of each row, # classifies each by length delta (>=50 bp -> INS, <=-50 bp -> DEL, # |d|<50 and max(len)>=50 -> CPX, else drop), then emits one row per # snarl (VCF line) with AC summed across passing alts. bash ~/kent/src/hg/makeDb/scripts/lrSv/lrSvAprBuild.sh mkdir -p /gbdb/hs1/lrSv /gbdb/hg38/lrSv ln -sf /hive/data/genomes/hg38/bed/lrSv/apr/apr.hs1.bb /gbdb/hs1/lrSv/apr.bb ln -sf /hive/data/genomes/hg38/bed/lrSv/apr/apr.hg38.bb /gbdb/hg38/lrSv/apr.bb ########## # 2026-04-21 Claude max # # cpc1Sv rebuilt as CPC-only (58 samples). The upstream VCF contains # 105 samples (58 CPC + 47 HPRC Phase 1). For this version we # identify the 58 CPC columns by sample name prefix (HIFI032* or # RY*), recompute AC/AN/NS from those GT columns only, and drop # snarls where no CPC sample carries any alt. HPRC-specific SVs are # therefore excluded; the HPRC contribution is already represented # in the HPRC SV tracks elsewhere in this lrSv supertrack. # # Pipeline (same build script, updated Python converter): cd /hive/data/genomes/hg38/bed/lrSv/cpc1 bash ~/kent/src/hg/makeDb/scripts/lrSv/lrSvCpc1Build.sh # hs1 sites: 46,092 (down from 97,205 combined) # hg38 lifted: 36,030 (down from 81,261); 10,062 unmapped