d77f68cb2aedf8aa2a4951671d9fd391b2eab153
markd
  Mon Apr 25 22:17:21 2022 -0700
added SGDP copy number tracks

diff --git src/hg/makeDb/doc/chm13v2.0userData/build.txt src/hg/makeDb/doc/chm13v2.0userData/build.txt
index 179dce6..6d3a109 100644
--- src/hg/makeDb/doc/chm13v2.0userData/build.txt
+++ src/hg/makeDb/doc/chm13v2.0userData/build.txt
@@ -297,30 +297,44 @@
 ----------------------------------------------------------------
 Arang Rhie
 
 doc https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/pattern/microsatellite.html
 
 GA https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/pattern/chm13v2.0.microsatellite.GA.128.wig
 TC https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/pattern/chm13v2.0.microsatellite.TC.128.wig
 GC https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/pattern/chm13v2.0.microsatellite.GC.128.wig
 AT https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/pattern/chm13v2.0.microsatellite.AT.128.wig
 
 # convert to bigWi
 for f in *.wig ; do wigToBigWig -clip $f ../ucscChromNames/t2t-chm13-v2.0.sizes  $(basename $f .wig).bw ; done
 pigz *.wig
 
 ================================================================
+* sgdpCopyNumber (2022-04-25 markd)
+----------------------------------------------------------------
+SGDP copy number estimates
+Mitchell R. Vollger, William Harvey
+
+https://eichlerlab.gs.washington.edu/help/mvollger/share/tracks/t2t-chm13-v2.0/SGDP_CN/hub.txt
+https://eichlerlab.gs.washington.edu/help/mvollger/share/tracks/t2t-chm13-v2.0/SGDP_CN/trackDb.t2t-chm13-v2.0.txt
+https://eichlerlab.gs.washington.edu/help/mvollger/share/tracks/t2t-chm13-v2.0/SGDP_CN/bigbed/description.html
+
+download the 348 bigBeds in trackDb from 
+  https://eichlerlab.gs.washington.edu/help/mvollger/share/tracks/t2t-chm13-v2.0/SGDP_CN/bigbed/
+
+
+================================================================
 pending:
 
 - ensembl:
   http://ftp.ebi.ac.uk/pub/databases/ensembl/hprc/y1_freeze/ contains all Y1 assemblies;
   http://ftp.ebi.ac.uk/pub/databases/ensembl/hprc/y1_freeze/GCA_009914755.4/ is CHM13v2
 
 - isoseq BAMs
   http://courtyard.gi.ucsc.edu/~mhauknes/T2T/t2t_Y/out-t2t-chrY-augPB/assemblyHub/CHM13/
   @PG   ID:minimap2   PN:minimap2   VN:2.22-r1105-dirty   CL:minimap2 -ax splice -f 1000 --sam-hit-only --secondary=no --eqx -K 100M -t 8 --cap-sw-mem=3g chm13v2.0.chrY.fasta HG002-NA24385-LCL-polished_isoforms_hq.fasta
   globus /HG002-IsoSeq
 
 - isoseq
     Fritz Sedlazeck  1 minute ago
     STUDY: PRJNA754107
      SAMPLE: GM27730 (SAMN20741798)