6f3383011d3d8aa64883b9437baec9440052046f
max
  Fri May 6 08:05:10 2022 -0700
adding chrX scores to gnomad constraints on hg38, refs #29026

diff --git src/hg/makeDb/doc/hg38/gnomad.txt src/hg/makeDb/doc/hg38/gnomad.txt
index 1146c5e..f262e85 100644
--- src/hg/makeDb/doc/hg38/gnomad.txt
+++ src/hg/makeDb/doc/hg38/gnomad.txt
@@ -205,19 +205,22 @@
 # sys 16m7.130s
 time (ls -1S hg38/genomes/chr*.bed |
     parallel --joblog join.run.log --max-procs 12 \\
         bedJoinTabOffset -verbose=2 -bedKey=3 gnomad.v3.1.1.details.pre.tab {} joined/{/}) &> bedJoinTabOffset.log &
 time sort --merge joined/*.bed | grep -v "^#" > gnomad.v3.1.1.genomes.joined.bed
 # real    16m4.876s
 # user    12m2.699s
 # 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