b98e1d0ccffb3a4c1d69f6c69ab98a842840aa57
angie
  Fri Apr 24 13:58:33 2020 -0700
Adding VCF subtrack for David: filter to recurrent bi-allelic variants only.  refs #25188

diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh
index 156b066..1b28d31 100755
--- src/hg/utils/otto/nextstrainNcov/doUpdate.sh
+++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh
@@ -34,57 +34,59 @@
 runDir=$ottoDir/$today
 cd $runDir
 chmod 444 ncov.$ncovTime.json
 ln -sf ncov.$ncovTime.json ncov.json
 
 #Generate bed and VCF files
 $ottoDir/nextstrain.py
 
 # bgzip & tabix the VCF files
 bgzip -f nextstrainSamples.vcf
 tabix -p vcf nextstrainSamples.vcf.gz
 for clade in A1a A2 A2a A3 A6 A7 B B1 B2 B4; do
   bgzip -f nextstrainSamples$clade.vcf
   tabix -p vcf nextstrainSamples$clade.vcf.gz
 done
+bgzip -f nextstrainRecurrentBiallelic.vcf
+tabix -p vcf nextstrainRecurrentBiallelic.vcf.gz
 
 # bigBed-ify the gene names, "clades" and discarded/blacklisted/informative tracks for David
 bedToBigBed -type=bed4 -tab -verbose=0 nextstrainGene.bed $chromSizes \
     nextstrainGene.bb
 
 sort -k2n,2n nextstrainClade.bed > nextstrainClade.sorted.bed
 bedToBigBed -as=$ottoDir/nextstrainClade.as -type=bed12+7 -tab -verbose=0 \
     nextstrainClade.sorted.bed $chromSizes \
     nextstrainClade.bb
 
 bedToBigBed -type=bed4 -tab -verbose=0 nextstrainDiscarded.bed $chromSizes \
     nextstrainDiscarded.bb
 
 bedToBigBed -type=bed4 -tab -verbose=0 nextstrainBlacklisted.bed $chromSizes \
     nextstrainBlacklisted.bb
 
 bedToBigBed -type=bed4 -tab -verbose=0 nextstrainInformative.bed $chromSizes \
     nextstrainInformative.bb
 
 # bigWig for the tree parsimony scores track for David
 bedGraphToBigWig nextstrainParsimony.bedGraph $chromSizes nextstrainParsimony.bw
 
 # Install
 ln -sf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
-    $runDir/nextstrainSamples*.vcf.gz{,.tbi} \
+    $runDir/nextstrain*.vcf.gz{,.tbi} \
     $runDir/nextstrain*.nh \
     $gbdbDir/
 
 # Install but don't archive (for now) the experimental tracks for David.
 ln -sf $runDir/nextstrain{Discarded,Blacklisted,Informative}.bb \
     $runDir/nextstrainParsimony.bw \
     $gbdbDir/
 
 # Archive
 mkdir -p $ottoDir/archive/$today
 cp -pf $runDir/nextstrainGene.bb $runDir/nextstrainClade.bb \
-    $runDir/nextstrainSamples*.vcf.gz{,.tbi} \
+    $runDir/nextstrain*.vcf.gz{,.tbi} \
     $runDir/nextstrain*.nh \
     $runDir/ncov.json \
     $ottoDir/archive/$today
 
 echo "Updated nextstrain/ncov `date` (ncov.json date $latestDate)"