4e6eb7db020f87bdc9f63f347cee9a080251f0fa
braney
  Wed May 1 15:00:06 2019 -0700
clean up GDC Cancer AS file

diff --git src/hg/makeDb/doc/hg38/gdcCancer.txt src/hg/makeDb/doc/hg38/gdcCancer.txt
index 3cc0d7f..2001087 100644
--- src/hg/makeDb/doc/hg38/gdcCancer.txt
+++ src/hg/makeDb/doc/hg38/gdcCancer.txt
@@ -1,17 +1,20 @@
 
 
 mkdir /cluster/data/hg38/bed/gdcCancer
 cd /cluster/data/hg38/bed/gdcCancer
 
 #go to https://portal.gdc.cancer.gov/repository?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.access%22%2C%22value%22%3A%5B%22open%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.analysis.workflow_type%22%2C%22value%22%3A%5B%22MuTect2%20Variant%20Aggregation%20and%20Masking%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_format%22%2C%22value%22%3A%5B%22MAF%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_type%22%2C%22value%22%3A%5B%22Masked%20Somatic%20Mutation%22%5D%7D%7D%5D%7D
 # add files to cart, click on cart, hit download button
 
 # press clinical button and select TSV.  Download will contain clinical.tsv exposure.tsv
 
 tar xvf gdc_download_20190408_221221.617568.tar.gz
 tar xvf clinical.cart.2019-04-22.tar.gz
 
 cancerMafToBigBed . clinical.tsv exposure.tsv gdcCancer.bb
 
+#rebuild the bb with a polished AS file
+bedToBigBed -as=$HOME/kent/src/hg/lib/gdcCancer.as -type=bed12+ -tab gdcCancer.s.bed /cluster/data/hg38/chrom.sizes gdcCancer.bb
+
 rm /gbdb/hg38/gdcCancer.bb
 ln -s `pwd`/gdcCancer.bb /gbdb/hg38