bab72b3c808c25df14fb563dc33336ff79a1f629
kuhn
  Tue Apr 26 15:14:18 2022 -0700
moved canFam3 evaSnp track to top level for consistency with Lous pipeline. combined html page to include some extra info that was in the canFam3 page

diff --git src/hg/makeDb/doc/canFam3.txt src/hg/makeDb/doc/canFam3.txt
index 4382ae6..6bc195b 100644
--- src/hg/makeDb/doc/canFam3.txt
+++ src/hg/makeDb/doc/canFam3.txt
@@ -1308,30 +1308,33 @@
 3492428 BROAD_VGB_CANINE_PON_SNP_DISCOVERY
 2458565 BROAD_DBSNP.2005.2.4.16.57
  697053 TIGR_1.0
  234166 BROAD_VGB_LYMPHOMA_SNP_DISCOVERY
    4202 DOG_GEN_LAB_1032011
      94 AMOUCD_MAL_20+TERV_1
 ...
 
 cat evaSnps4.bed | awk '{print $10}' | sed -e "s/,/\n/g" | sort | uniq -c | sort -r
 # 52
 
 # 52 different submitters.  most from a few places, mostly the Broad
 
 ##############################################################################
 # canFam3 EVA SNPs (European Variation Archive) (DONE 2022-03-21 - b0b)
+# NOTE:  superceded by Lou's pipeline for consistency.
+#   doc'd for multiple assemblies at: evaSnp3.txt
+#
 # adding VAI annotations
 # redoing the track after talking with Lou and standardinzing on data fields after VAI step
 
 # canFam3.1 = GCA_000002285.2
 
 # get files (EVA Release 3)
 cd /hive/data/outside/dogSnps/release3 
 wget https://ftp.ebi.ac.uk/pub/databases/eva/rs_releases/release_3/by_species/canis_lupus_familiaris/GCA_000002285.2/GCA_000002285.2_current_ids.vcf.gz
 
 # what is .csi file???? 
 # https://ftp.ebi.ac.uk/pub/databases/eva/rs_releases/release_3/by_species/canis_lupus_familiaris/GCA_000002285.2/GCA_000002285.2_current_ids.vcf.gz.csi
 
 # previous:
 #  5655125 evaRsIDs
 #  same number in this release
@@ -2035,24 +2038,16 @@
 # complex_transcript_variant,
 # intron_variant,
 # non_coding_transcript_exon_variant,
 # upstream_gene_variant,
 # downstream_gene_variant,
 # intergenic_variant,
 # no_sequence_alteration,
 
 # add new filter lines to trackDb
 # filterValues.varClass (new name for same field -- orig EVA class
 # filterValues.ucscClass missense_variant,frameshift_variant,inframe_deletion,inframe_insertion,initiator_codon_variant,stop_gained,stop_lost,splice_acceptor_variant,splice_donor_variant,splice_region_variant,exon_loss_variant,coding_sequence_variant,5_prime_UTR_variant,3_prime_UTR_variant,NMD_transcript_variant,synonymous_variant,stop_retained_variant,complex_transcript_variant,non_coding_transcript_exon_variant,intron_variant,upstream_gene_variant,downstream_gene_variant,intergenic_variant,no_sequence_alteration,  
 
 # drop old filter lines (no longer using RS_VALIDATED field
 filterValues.valid No,Yes
 
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 ##############################################################################