a9a7db4b5a18b03edea1c8c8df30a5a03c610d25 chmalee Wed Nov 1 16:30:45 2023 -0700 Staging gnomad v4 vcfs track, refs #32545 diff --git src/hg/makeDb/doc/hg38/gnomad.txt src/hg/makeDb/doc/hg38/gnomad.txt index f262e85..8eef883 100644 --- src/hg/makeDb/doc/hg38/gnomad.txt +++ src/hg/makeDb/doc/hg38/gnomad.txt @@ -212,15 +212,48 @@ # sys 6m30.244s # and lastly turn the merged bed into a bigBed: time (bedToBigBed -type=bed9+15 -tab -as=genomes.as -extraIndex=name,rsId,_displayName gnomad.v3.1.1.genomes.joined.bed /hive/data/genomes/hg38/chrom.sizes genomes.bb) &> bigBed.log & # Max Tue Apr 5 04:14:40 PDT 2022 - adding mutation constraint subtrack cd /hive/data/genomes/hg38/bed/gnomad/constraint # Downloaded BED file from https://www.biorxiv.org/content/10.1101/2022.03.20.485034v1.supplementary-material # got chrX scores from konrad.j.karczewski@gmail.com because they feel unsure about them cat Supplementary_Data_2.bed constraint_z_genome_1kb_chrx.bed > mutConstraint.bed bedSort mutConstraint.bed mutConstraint.bed bedGraphToBigWig *.bed ../../../chrom.sizes mutConstraint.bw bedGraphToBigWig *.bed ../../../chrom.sizes mutConstraint.bw +############################################################################## +# gnomAD v4 - Nov 1, 2023 - ChrisL - DONE +############################################################################## +# See /hive/data/outside/gnomAD.4/make.txt for how to download +# the new version +# Make the work dir: +mkdir -p /hive/data/inside/gnomAD/v4 +cd /hive/data/inside/gnomAD/v4 + +# for each vcf in the download dirs, install files into /gbdb and load up a table with the pointers +gbdbPath="/gbdb/hg38/gnomAD/v4/" +dataPath="/hive/data/outside/gnomAD.4/" +for tbl in exomes genomes +do + mkdir -p ${gbdbPath}${tbl} + ln -s ${dataPath}${tbl}/*.vcf.bgz* ${gbdbPath}${tbl} + cp /dev/null ${tbl}.txt + if [ ${tbl} == "exomes" ]; then + for c in {1..22} X Y + do + f=${gbdbPath}${tbl}/gnomad.exomes.v4.0.sites.chr${c}.vcf.bgz + echo -e "${f}\tchr${c}" >> ${tbl}.txt + done + else + for c in {1..22} X + do + f=${gbdbPath}${tbl}/gnomad.genomes.v4.0.sites.chr${c}.vcf.bgz + echo -e "${f}\tchr${c}" >> ${tbl}.txt + done + fi +done +hgLoadSqlTab hg38 gnomadGenomesV4 ~/kent/src/hg/lib/bbiChroms.sql genomes.txt +hgLoadSqlTab hg38 gnomadExomesV4 ~/kent/src/hg/lib/bbiChroms.sql exomes.txt