modified: cre.R

modified: cre.annotate_str.sh modified: cre.phenomecentral.upload_vcf_attachment.prototype.py modified: vcf.gatk.get_depth.sh
naumenko-sa · Nov 3, 2017 · 5e771b4 · 5e771b4
1 parent a71af1f
commit 5e771b4
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Showing 4 changed files with 5 additions and 4 deletions.
diff --git a/cre.R b/cre.R
@@ -629,8 +629,8 @@ args = commandArgs(trailingOnly = T)
 family = args[1]
 
 # DEBUG
- setwd("~/cluster/validation/nist_ashkenazim_trio/")
- family="Ashkenazim"
+# setwd("~/cluster/validation/nist_ashkenazim_trio/")
+# family="Ashkenazim"
 
 setwd(family)
 

diff --git a/cre.annotate_str.sh b/cre.annotate_str.sh
@@ -2,7 +2,7 @@
 
 #use cre.annotate_str.sh vcf_from_lobstr.vcf
 
-bname=`echo $1 | sed s/.vcf//`
+bname=`basename $1 .vcf`
 
 cat $1 | grep "^#" > $bname.sorted.vcf
 #sometimes lobSTR gives you unsorted vcf for some reason

diff --git a/cre.phenomecentral.upload_vcf_attachment.prototype.py b/cre.phenomecentral.upload_vcf_attachment.prototype.py
diff --git a/vcf.gatk.get_depth.sh b/vcf.gatk.get_depth.sh
@@ -3,4 +3,5 @@
 bname=`echo $1 | sed s/.vcf.gz//`
 
 gatk -R ~/work/tools/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -T VariantsToTable -V $1 \
-     -F CHROM -F POS -F REF -F ALT -F DP -GF DP -GF AD -GF GT -o $bname.table --allowMissingData 
+     -F CHROM -F POS -F REF -F ALT -F DP -GF DP -GF AD -GF GT -o $bname.table 
+    #--allowMissingData -not used since gatk3.8