modified: cre.rtg.validate.sh

	deleted:    cre.validation.sh

cre.rtg.validate.sh

@@ -1,24 +1,24 @@
 #!/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 \
    -t /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/rtg/GRCh37.sdf \
    -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
-