8ada62f0cad845d55480e7e47dcab4b246736383
max
  Fri Jan 17 09:44:58 2020 -0800
after feedback from Terence, fix RefSeq Select to include MANE and update the docs page. refs #24787

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index b92b2af..18e949b 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -33953,21 +33953,21 @@
     #     )
 
     # now we can make the bigBed:
     ./aaToGenomic.py trimmedUtrs.txt 148353-3/Table_S4.csv | sort -k1,1 -k2,2n > missenseConstrained.bed
     bedToBigBed -tab -type=bed12+5 -as=missenseBed.as missenseConstrained.bed /hive/data/genomes/hg19/chrom.sizes missenseConstrained.bb
     # pass1 - making usageList (24 chroms): 5 millis
     # pass2 - checking and writing primary data (6507 records, 17 fields): 134 millis
     # only a few genes:
     cut -f13 missenseConstrained.bed | sort | uniq | wc -l
     # 2700
     ln -s /gbdb/hg19/gnomAD/missenseConstrained.bb missenseConstrained.bb
 
 ##############################################################################
 # adding RefSeq Select to NCBIRefSeq, Max, Feb 17 2020
 cd /hive/data/genomes/hg19/bed/ncbiRefSeq.p13.2019-11-21
-zcat download/*_genomic.gff.gz | grep 'tag=RefSeq Select'  | cut -f9- | tr ';' '\n' | grep Name= | grep -v NP_ | cut -d= -f2 | sort -u > refseqSelectTranscripts.txt
+zcat download/*_genomic.gff.gz | egrep 'tag=(RefSeq|MANE) Select'  | cut -f9- | tr ';' '\n' | grep Name= | grep -v NP_ | cut -d= -f2 | sort -u > refseqSelectTranscripts.txt
 cat process/hg19.curated.gp | fgrep -f refseqSelectTranscripts.txt - > refseqSelect.curated.gp
 hgLoadGenePred -genePredExt hg19 ncbiRefSeqSelect refseqSelect.curated.gp
 wc -l refseqSelect.curated.gp
-9355 refseqSelect.curated.gp
+21436 refseqSelect.curated.gp
 ##############################################################################