f058c8fe4601b223ff47468eb3525c05ccd03850 max Wed Apr 22 09:17:17 2026 -0700 srSv: new short-read SV supertrack, split out of lrSv Move the three short-read SV/CNV subtracks (abelSv, onekg3202Sr, tommoJpCnv) out of the Long-read SV supertrack into a new sibling supertrack srSv (Short-read SVs), so the lrSv collection contains only long-read callsets. Filter fields (svType, svLen, insLen, AC) are mirrored at the srSv supertrack level to keep the UX parallel to lrSv. - trackDb: new human/srSv.ra with the three subtrack stanzas and updated /gbdb/$D/srSv/... bigDataUrls; corresponding stanzas removed from human/lrSv.ra. human/trackDb.ra now includes srSv.ra. Also a new human/srSv.html overview page; the SR rows and SR-specific paragraphs removed from human/lrSv.html. - Scripts: abelSv/{abelSv.as,vcfToBed.py,build.sh} and lrSv/ {lrSv1kg3202Sr*, lrSvTommoJpCnvVcfToBedGraph.py} moved to scripts/srSv/ with git mv (history preserved) and renamed to drop the "lrSv" prefix. Internal path references in abelSvBuild.sh and abelSvVcfToBed.py updated. - makeDoc: doc/hg38/abelSv.txt renamed to doc/hg38/srSv.txt and extended with the onekg3202Sr and tommoJpCnv sections moved from lrSv.txt. lrSv.txt leaves a pointer. - Data: /hive/data/genomes/hg38/bed/{abelSv,lrSv/onekg3202sr, lrSv/tommoJpCnv} moved to /hive/data/genomes/hg38/bed/srSv/*. /gbdb/hg38/lrSv/{onekg3202sr.bb,tommoJpCnv{Loss,Gain}.bw} and /gbdb/hg38/abelSv/ removed and re-linked under /gbdb/hg38/srSv/. refs #36258 diff --git src/hg/makeDb/doc/hg38/srSv.txt src/hg/makeDb/doc/hg38/srSv.txt new file mode 100644 index 00000000000..c5b97e2fc54 --- /dev/null +++ src/hg/makeDb/doc/hg38/srSv.txt @@ -0,0 +1,99 @@ +# Short-read SV supertrack (srSv) - companion to the Long-read SV supertrack. +# +# This file documents how each short-read SV/CNV subtrack under the srSv +# supertrack was built. All tracks are hg38-only. Build scripts and +# autoSql schemas live in ~/kent/src/hg/makeDb/scripts/srSv/. + +########## +# 2026-04-20: CCDG 17,795 SVs (abelSv) - Abel et al 2020 Nature (Claude) +# +# Paper: Abel HJ et al., Nature 583:83-89 (2020), doi 10.1038/s41586-020-2371-0 +# Data : https://github.com/hall-lab/sv_paper_042020 +# Supplementary_File_1.zip (B38 native callset, 14,623 samples) +# Supplementary_File_2.zip (B37 callset, 8,417 samples) +# +# The two public callsets are non-overlapping in SVs but share 5,245 samples. +# For the hg38 track we display B38 natively and lift B37 coordinates to +# hg38 with the standard UCSC liftOver chain. B37 variants that do not lift +# (626 of 280,518 primary records) are dropped. + +mkdir -p /hive/data/genomes/hg38/bed/srSv/abelSv +cd /hive/data/genomes/hg38/bed/srSv/abelSv + +# Fetch site-frequency callsets +wget -c https://raw.githubusercontent.com/hall-lab/sv_paper_042020/master/Supplementary_File_1.zip +wget -c https://raw.githubusercontent.com/hall-lab/sv_paper_042020/master/Supplementary_File_2.zip +unzip -o Supplementary_File_1.zip # -> Build38.public.v2.{vcf,bedpe}.gz +unzip -o Supplementary_File_2.zip # -> Build37.public.v2.{vcf,bedpe}.gz + +# Convert, lift B37, merge, build bigBed. +# The script parses each VCF, collapses detailed MEI subtypes +# (e.g. <DEL:ME:LINE|L1|L1HS>) to SVTYPE=MEI, drops SECONDARY BND records +# so each translocation pair appears only once, and emits one bed14+ +# line per variant with per-population AC/AN, MSQ, etc. +bash ~/kent/src/hg/makeDb/scripts/srSv/abelSvBuild.sh + +# Result: +# B38 bed : 458,106 records +# B37 bed : 280,518 records (before lift) +# B37 lifted : 279,892 records (626 unmapped) +# abelSv.bb : 737,998 records + +# Symlink for trackDb +mkdir -p /gbdb/hg38/srSv +ln -sf /hive/data/genomes/hg38/bed/srSv/abelSv/abelSv.bb /gbdb/hg38/srSv/abelSv.bb + + +########## +# 1KG 3202 SR SVs (onekg3202Sr) - Byrska-Bishop et al 2022 Cell +# +# Paper: Byrska-Bishop M, Cell 185(18):3426-3440 (2022) +# doi 10.1016/j.cell.2022.08.004 +# Data : 1000 Genomes 3202-sample GATK-SV freeze V3 VCF with allele +# frequencies (wAF suffix). +# VCF: 1KGP_3202.gatksv_svtools_novelins.freeze_V3.wAF.vcf.gz +# +# Source VCF at /hive/data/genomes/hg38/bed/srSv/onekg3202sr/. +# 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. + +cd /hive/data/genomes/hg38/bed/srSv/onekg3202sr +python3 ~/kent/src/hg/makeDb/scripts/srSv/onekg3202SrVcfToBed.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/srSv/onekg3202Sr.as \ + -tab onekg3202sr.sorted.bed /hive/data/genomes/hg38/chrom.sizes \ + onekg3202sr.bb + +ln -sf /hive/data/genomes/hg38/bed/srSv/onekg3202sr/onekg3202sr.bb \ + /gbdb/hg38/srSv/onekg3202sr.bb + + +########## +# ToMMo 48K CNV SR (tommoJpCnv) - jMorp 48KJPN-CNV Frequency Panel +# +# Data : jMorp release 20230828, tommo-jcnvv1-20230828-GRCh38.vcf.gz +# 48,874 Japanese individuals, short-read WGS, GATK germline CNV. +# Source under /hive/data/genomes/hg38/bed/srSv/tommoJpCnv/. +# +# The input VCF provides per-sample copy-number calls in 1 kb bins. +# Convert to two bigWig tracks (samples with CN<2 loss; samples with +# CN>2 gain), rendered as a transparent multiWig overlay. + +cd /hive/data/genomes/hg38/bed/srSv/tommoJpCnv +python3 ~/kent/src/hg/makeDb/scripts/srSv/tommoJpCnvVcfToBedGraph.py \ + tommo-jcnvv1-20230828-GRCh38.vcf.gz \ + tommoJpCnvLoss.bedGraph tommoJpCnvGain.bedGraph +for k in Loss Gain; do + bedSort tommoJpCnv${k}.bedGraph tommoJpCnv${k}.sorted.bedGraph + bedGraphToBigWig tommoJpCnv${k}.sorted.bedGraph \ + /hive/data/genomes/hg38/chrom.sizes tommoJpCnv${k}.bw +done + +ln -sf /hive/data/genomes/hg38/bed/srSv/tommoJpCnv/tommoJpCnvLoss.bw \ + /gbdb/hg38/srSv/tommoJpCnvLoss.bw +ln -sf /hive/data/genomes/hg38/bed/srSv/tommoJpCnv/tommoJpCnvGain.bw \ + /gbdb/hg38/srSv/tommoJpCnvGain.bw