cd5b2b3bcde639cf2242c96fb0afcc016bdf77b1
kuhn
  Wed Mar 2 16:33:34 2022 -0800
adapting a line to proper format

diff --git src/hg/makeDb/doc/canFam3.txt src/hg/makeDb/doc/canFam3.txt
index 7e8ca71..eba5402 100644
--- src/hg/makeDb/doc/canFam3.txt
+++ src/hg/makeDb/doc/canFam3.txt
@@ -1175,31 +1175,31 @@
 # vcfToBed requires a tabix
 tabix -p vcf dogSNPs.vcf.gz
 
 # make a bed file with 3 useful flags
 vcfToBed dogSNPs.vcf.gz dogSNPs3Flags -fields=VC,SID,RS_VALIDATED
 # VC=Variant Class, SID=Submitter ID,  RS_VALIDATED=validated from dbSNP 
 
 wc -l *bed
 # 5655126 dogSNPs3Flags.bed
 wc -l *vcf
 # 5655174 GCA_000002285.2_current_ids.vcf
 
 # sort file
 bedSort dogSNPs3Flags.bed dogSNPs3Flags.bed
 
-[kuhn@hgwdev release3]$ head -2 dogSNPs3Flags.bed
+head -2 dogSNPs3Flags.bed
 #chrom  chromStart      chromEnd        name    score   strand  thickStart      thickEnd        itemRgb ref     alt     FILTER  VC      SID     RS_VALIDATED
 #chr1    111     112     rs850979046     0       .       111     112     0,0,0   A       G       .       SO:0001483      BROAD_VGB_CANINE_PON_SNP_DISCOVERY
 
 # drop unnecessary fields:  thickStart      thickEnd        itemRgb 
 cat dogSNPs3Flags.bed \
   | awk -F"\t" '{print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$10"\t"$11"\t"$13"\t"$14"\t"$15}' \
   > evaSnps1.bed
 
 head evaSnps1.bed
 #chrom  chromStart      chromEnd        name    score   strand  ref     alt     VC      SID     RS_VALIDATED
 # chr1    111     112     rs850979046     0       .       A       G       SO:0001483      BROAD_VGB_CANINE_PON_SNP_DISCOVERY
 
 # add "No" to last column where needed (RS_VALIDATED)
 cat evaSnps1.bed \
   | awk '{if ($11 != "Yes") { print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\tNo"; } \