4f8f8773bec66a9e993e9897e0b032c6e97dead8 max Fri May 15 10:12:29 2026 -0700 mei: add HMEID, SweGen, and euL1db subtracks Three new MEI catalogues under the existing mei superTrack: meiHmeid (hg38) 36,699 MELT MEIs from HMEID v1.1 (NyuWa+1KGP, 5,675 individuals, Niu et al. 2022, PMID 35212372). Site-level VCF; per-cohort and per-1KGP super- population AC/AN/AF; SVTYPE Alu/L1/SVA/HERVK. meiSwegen (hg38 lifted) 18,090 MELT MEIs from the SweGen 1,000-sample Swedish cohort (Ameur 2017, PMID 28832569; Gardner 2017, PMID 28855259). Built on hg19, liftOver to hg38 (10 unmapped). tableBrowser off per SweGen distribution terms. meiEul1db (hg19+hg38) 8,988 curated L1-HS insertion polymorphisms (MRIPs) from euL1db v1.00 (Mir 2015, PMID 25352549), aggregating 142,495 sample-level SRIPs across 32 published studies. Coloured by lineage (germline/somatic/mixed). Built on hg19, liftOver to hg38 (3 unmapped). Helman2014 used numeric chrom names (23=X, 24=Y) which are renamed during the build. meiEul1dbRef (hg19+hg38) 1,540 reference-genome L1-HS copies catalogued by euL1db (companion to meiEul1db). Single shared mei.ra (in human/) uses $D substitution so each stanza serves both assemblies where applicable. refs #37524 diff --git src/hg/makeDb/doc/hg38/mei.txt src/hg/makeDb/doc/hg38/mei.txt index 8e81438786a..14a96541bec 100644 --- src/hg/makeDb/doc/hg38/mei.txt +++ src/hg/makeDb/doc/hg38/mei.txt @@ -87,15 +87,188 @@ python3 ~/kent/src/hg/makeDb/scripts/mei/meiDeepmei1kgVcfToBed.py \ merge_1000g.latested.vcf.gz \ /hive/data/genomes/hg38/chrom.sizes \ deepmei.bed # -> Read 91617 records, wrote 91617, skipped 0 + 0 + 0 # Class distribution: Alu 68282, L1 16891, SVA 6444. sort -k1,1 -k2,2n deepmei.bed > deepmei.sorted.bed bedToBigBed -tab \ -as=$HOME/kent/src/hg/makeDb/scripts/mei/meiDeepmei1kg.as \ -type=bed9+7 \ deepmei.sorted.bed \ /hive/data/genomes/hg38/chrom.sizes \ deepmei1kg.bb + +############################################################ +# 2026-05-12 Claude (max) - HMEID v1.1 (hg38 only) +# Source: Niu et al. 2022, Nucleic Acids Research, PMID 35212372 +# http://bigdata.ibp.ac.cn/HMEID/ + +# HMEID is a site-level catalogue of 36,699 non-reference MEIs called +# by MELT v2.1.5 on Illumina short-read WGS of 5,675 individuals: +# 2,998 NyuWa (Chinese, ~26.2x) + 2,677 1000 Genomes (~7.4x), aligned +# to GRCh38. The VCF carries per-cohort (NyuWa, 1KGP) and per-1KGP- +# super-population (AFR, AMR, EAS, EUR, SAS) AC/AN/AF in INFO; there +# are no per-sample genotype columns. SVTYPE is one of ALU/LINE1/SVA/ +# HERVK, plus the MELT TSD and ASSESS fields. + +mkdir -p /hive/data/genomes/hg38/bed/mei/hmei +cd /hive/data/genomes/hg38/bed/mei/hmei + +wget http://bigdata.ibp.ac.cn/HMEID/static/download/MEI.GRCh38.HMEIDv1.1.vcf.gz +wget http://bigdata.ibp.ac.cn/HMEID/static/download/sample_info.HMEIDv1.1.txt.gz + +# Convert site-level VCF (36699 MEIs) to bed9+27. +# Source: ~/kent/src/hg/makeDb/scripts/mei/meiHmeidVcfToBed.py +python3 ~/kent/src/hg/makeDb/scripts/mei/meiHmeidVcfToBed.py \ + MEI.GRCh38.HMEIDv1.1.vcf.gz \ + /hive/data/genomes/hg38/chrom.sizes \ + meiHmeid.bed +# -> Read 36699 records, wrote 36699, skipped 0 + 0 + 0 +# Class distribution: Alu 26553, HERVK 126, L1 7353, SVA 2667. + +sort -k1,1 -k2,2n meiHmeid.bed > meiHmeid.sorted.bed + +bedToBigBed -tab \ + -as=$HOME/kent/src/hg/makeDb/scripts/mei/meiHmeid.as \ + -type=bed9+27 \ + meiHmeid.sorted.bed \ + /hive/data/genomes/hg38/chrom.sizes \ + meiHmeid.bb + +############################################################ +# 2026-05-13 Claude (max) - SweGen MELT MEI callset (hg38, lifted from hg19) +# Source: Ameur et al. 2017, Eur J Hum Genet, PMID 28832569 (SweGen cohort) +# Gardner et al. 2017, Genome Res, PMID 28855259 (MELT tool) +# https://swefreq.nbis.se/dataset/SweGen + +# Site-level MELT v2.0.2 MEI callset on 1,000 Swedish WGS samples +# (SweGen, Illumina HiSeq X, 150 bp PE, BWA-MEM v0.7.12 to GRCh37). +# The VCF has no per-sample columns; INFO carries MELT_AN (allele +# count, despite the name) and MELT_AF (allele frequency) plus the +# usual MELT fields SVTYPE/SVLEN/TSD/ASSESS/MEIINFO/INTERNAL. +# Coordinates are GRCh37 with contig names like '1' (no chr prefix); +# we add chr in Python and then liftOver hg19 -> hg38. + +mkdir -p /hive/data/genomes/hg38/bed/mei/swegen +cd /hive/data/genomes/hg38/bed/mei/swegen +# Source VCF must be requested from https://swefreq.nbis.se/dataset/SweGen/download +# (Swegen_MELT_16032018.zip); place MELT_SWEGEN.20180314.ALU_HERVK_LINE1_SVA.vcf +# under Swegen_MELT_16032018/. + +# Parse the VCF to a bed9+9 file with GRCh37 coords (adds chr prefix). +# Source: ~/kent/src/hg/makeDb/scripts/mei/meiSwegenVcfToBed.py +python3 ~/kent/src/hg/makeDb/scripts/mei/meiSwegenVcfToBed.py \ + Swegen_MELT_16032018/MELT_SWEGEN.20180314.ALU_HERVK_LINE1_SVA.vcf \ + meiSwegen.hg19.bed +# -> Read 18100 records, wrote 18100, skipped 0 (unknown SVTYPE) +# Class distribution: Alu 14467, HERVK 73, L1 2429, SVA 1131. + +# Lift to hg38 (-tab -bedPlus=9 to keep extra fields intact). +liftOver -tab -bedPlus=9 \ + meiSwegen.hg19.bed \ + /gbdb/hg19/liftOver/hg19ToHg38.over.chain.gz \ + meiSwegen.hg38.bed \ + meiSwegen.unmapped +# -> 18090 mapped, 10 unmapped (all "Deleted in new"). + +sort -k1,1 -k2,2n meiSwegen.hg38.bed > meiSwegen.sorted.bed + +bedToBigBed -tab \ + -as=$HOME/kent/src/hg/makeDb/scripts/mei/meiSwegen.as \ + -type=bed9+9 \ + meiSwegen.sorted.bed \ + /hive/data/genomes/hg38/chrom.sizes \ + meiSwegen.bb + +############################################################ +# 2026-05-13 Claude (max) - euL1db (hg19 + hg38 by liftOver) +# Source: Mir et al. 2015, Nucleic Acids Research, PMID 25352549 +# http://eul1db.unice.fr/ (Download tab -> eul1db.zip) + +# euL1db is a curated database of L1-HS retrotransposon insertion +# polymorphisms catalogued from 32 published studies (~140k sample-level +# SRIPs aggregating into ~9k non-redundant MRIPs). The original +# coordinates are hg19. We build the bigBed on hg19 from the MRIP table +# joined with SRIP/Sample/Individual/Study/Methods, then liftOver to +# hg38. A second small bigBed for the reference-genome L1HS catalogue +# (ReferenceL1HS.txt) is built and lifted the same way. + +# Source files (released as eul1db.zip, version 1.00, 2014-10-14): +# Family.txt Individuals.txt MRIP.txt Methods.txt ReferenceL1HS.txt +# SRIP.txt Samples.txt Study.txt +# We keep the source under hg38/bed/mei/eul1db (where it was first placed) +# and the hg19 build outputs under hg19/bed/mei/eul1db. + +mkdir -p /hive/data/genomes/hg19/bed/mei/eul1db +cd /hive/data/genomes/hg19/bed/mei/eul1db + +# 1) Build hg19 MRIP bigBed (8,991 MRIPs in the source; chr23/chr24 in +# Helman2014 rows are renamed to chrX/chrY in the script). +# Source: ~/kent/src/hg/makeDb/scripts/mei/meiEul1dbToBed.py +python3 ~/kent/src/hg/makeDb/scripts/mei/meiEul1dbToBed.py \ + --src /hive/data/genomes/hg38/bed/mei/eul1db \ + --chrom-sizes /hive/data/genomes/hg19/chrom.sizes \ + -o eul1db.hg19.bed +# -> SRIPs read: 142,495; MRIPs read: 8,991; MRIPs written: 8,991 +# -> chr23/24 renamed to chrX/chrY: 85; no chrom or range skips. + +sort -k1,1 -k2,2n eul1db.hg19.bed > eul1db.hg19.sorted.bed + +bedToBigBed -tab \ + -as=$HOME/kent/src/hg/makeDb/scripts/mei/meiEul1db.as \ + -type=bed9+19 \ + eul1db.hg19.sorted.bed \ + /hive/data/genomes/hg19/chrom.sizes \ + eul1db.hg19.bb + +# 2) Build hg19 reference-L1HS bigBed (1,544 elements). +# Source: ~/kent/src/hg/makeDb/scripts/mei/meiEul1dbRefToBed.py +python3 ~/kent/src/hg/makeDb/scripts/mei/meiEul1dbRefToBed.py \ + --src /hive/data/genomes/hg38/bed/mei/eul1db \ + --chrom-sizes /hive/data/genomes/hg19/chrom.sizes \ + -o eul1dbRef.hg19.bed +# -> Reference L1HS read: 1,544; written: 1,544 (all chroms in hg19). + +sort -k1,1 -k2,2n eul1dbRef.hg19.bed > eul1dbRef.hg19.sorted.bed + +bedToBigBed -tab \ + -as=$HOME/kent/src/hg/makeDb/scripts/mei/meiEul1dbRef.as \ + -type=bed9+6 \ + eul1dbRef.hg19.sorted.bed \ + /hive/data/genomes/hg19/chrom.sizes \ + eul1dbRef.hg19.bb + +# 3) liftOver to hg38 (-tab -bedPlus=9 to preserve extra fields). +liftOver -tab -bedPlus=9 \ + eul1db.hg19.sorted.bed \ + /gbdb/hg19/liftOver/hg19ToHg38.over.chain.gz \ + eul1db.hg38.bed eul1db.hg38.unmapped +# -> 8,988 mapped, 3 unmapped (1 "Deleted in new", 1 "Partially deleted", +# 1 "Deleted in new" on chr13/chrX). 99.97% mapped. + +liftOver -tab -bedPlus=9 \ + eul1dbRef.hg19.sorted.bed \ + /gbdb/hg19/liftOver/hg19ToHg38.over.chain.gz \ + eul1dbRef.hg38.bed eul1dbRef.hg38.unmapped +# -> 1,540 mapped, 4 unmapped (2 "Split in new", 2 "Partially deleted"). + +# 4) Build hg38 bigBeds (written to hg38/bed/mei/eul1db/ next to source). +sort -k1,1 -k2,2n eul1db.hg38.bed \ + > /hive/data/genomes/hg38/bed/mei/eul1db/eul1db.hg38.sorted.bed +bedToBigBed -tab \ + -as=$HOME/kent/src/hg/makeDb/scripts/mei/meiEul1db.as \ + -type=bed9+19 \ + /hive/data/genomes/hg38/bed/mei/eul1db/eul1db.hg38.sorted.bed \ + /hive/data/genomes/hg38/chrom.sizes \ + /hive/data/genomes/hg38/bed/mei/eul1db/eul1db.hg38.bb + +sort -k1,1 -k2,2n eul1dbRef.hg38.bed \ + > /hive/data/genomes/hg38/bed/mei/eul1db/eul1dbRef.hg38.sorted.bed +bedToBigBed -tab \ + -as=$HOME/kent/src/hg/makeDb/scripts/mei/meiEul1dbRef.as \ + -type=bed9+6 \ + /hive/data/genomes/hg38/bed/mei/eul1db/eul1dbRef.hg38.sorted.bed \ + /hive/data/genomes/hg38/chrom.sizes \ + /hive/data/genomes/hg38/bed/mei/eul1db/eul1dbRef.hg38.bb