From 9cf3d2f7ff6ef3be90d99c0d6d431d3df4a7021c Mon Sep 17 00:00:00 2001
From: naumenko-sa <evolgenomicslab@gmail.com>
Date: Wed, 23 Jan 2019 20:43:00 -0500
Subject: [PATCH] 	modified:   cre.rtg.validate.sh 	deleted:   
 cre.validation.sh

---
 cre.rtg.validate.sh | 14 +++++++-------
 cre.validation.sh   | 13 -------------
 2 files changed, 7 insertions(+), 20 deletions(-)
 delete mode 100755 cre.validation.sh

diff --git a/cre.rtg.validate.sh b/cre.rtg.validate.sh
index 229654a..95ed126 100755
--- a/cre.rtg.validate.sh
+++ b/cre.rtg.validate.sh
@@ -1,14 +1,15 @@
 #!/bin/bash
-# validate vcf file against genome in a bottle calls for NA12878
-# based on bcbio logs
+# validate a vcf file against genome in a bottle calls for NA12878
+# $1 - file.vcf.gz
+# $2 - regions.bed
 
 # rtg manual
 # https://github.com/RealTimeGenomics/rtg-tools/blob/master/installer/resources/tools/RTGOperationsManual.pdf
 
-#bedtools intersect -nonamecheck -a NA12878-sort-callable_sample.bed -b GiaB_v2_19_regions.bed > NA12878-sort-callable_sample-NA12878-wrm.bed
+# bedtools intersect -nonamecheck -a NA12878-sort-callable_sample.bed -b GiaB_v2_19_regions.bed > NA12878-sort-callable_sample-NA12878-wrm.bed
 
-#uses PASS variants only
-   export RTG_JAVA_OPTS='-Xms750m' && export RTG_MEM=9100m && \
+# uses PASS variants only
+export RTG_JAVA_OPTS='-Xms750m' && export RTG_MEM=9100m && \
    rtg vcfeval --threads 5 -b /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/validation/giab-NA12878/truth_small_variants.vcf.gz \
    --bed-regions $2 \
    -c $1 \
@@ -16,9 +17,8 @@
    -o rtg --vcf-score-field='GQ' 
 #   --all-records
 
-for f in {tp-baseline,fp,fn};
+for f in {tp-baseline,fp,fn}
 do
     echo snp $f `bcftools view --types snps rtg/$f.vcf.gz | grep -vc "^#"` >> $1.stat
     echo indels $f `bcftools view --exclude-types snps rtg/$f.vcf.gz | grep -vc "^#"` >> $1.stat
 done
-
diff --git a/cre.validation.sh b/cre.validation.sh
deleted file mode 100755
index 39b8c34..0000000
--- a/cre.validation.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/bash
-
-export PATH=/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/bin:$PATH &&  export RTG_JAVA_OPTS='-Xms750m' && export RTG_MEM=10000m && rtg vcfeval --threads 1  \
-    -b /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/validation/giab-NA12878/truth_small_variants.vcf.gz \
-    --bed-regions /hpf/largeprojects/ccmbio/naumenko/validation/lynette/work/validate/NA12878-1/ensemble/NA12878-1-sort-callable_sample-NA12878-1-ensemble-wrm.bed \
-    -c $1 \
-    -t /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/rtg/GRCh37.sdf -o rtg --vcf-score-field='GQ'
-
-for f in {tp,fp,fn};
-do
-    echo snp $f `bcftools view --types snps rtg/$f.vcf.gz | grep -vc "^#"` >> $1.stat
-    echo indels $f `bcftools view --exclude-types snps rtg/$f.vcf.gz | grep -vc "^#"` >> $1.stat
-done