modified: cre.vep.sh

naumenko-sa · Jun 11, 2018 · d16d015 · d16d015
1 parent 7086f63
commit d16d015
Showing 1 changed file with 11 additions and 5 deletions.
diff --git a/cre.vep.sh b/cre.vep.sh
@@ -54,13 +54,19 @@ bname=`basename $vcf .vcf.gz`
 #    --plugin SpliceRegion --sift b --polyphen b --hgvs --shift_hgvs 1 --merged \
 #    | sed '/^#/! s/;;/;/g' | bgzip -c > $bname.vepeffects.vcf.gz
 
-unset PERL5LIB && export PATH=/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/bin:$PATH && /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/bin/vep --vcf -o stdout \
-    -i $vcf --fork 5 --species homo_sapiens --no_stats --cache --offline --dir /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/vep --symbol --numbers --biotype --total_length \
+#find reference
+reference=`which gatk-launch | sed s/"bin\/gatk-launch"/"bcbio\/genomes\/Hsapiens\/GRCh37"/`
+bcbio_reference=`which gatk-launch | sed s/"bin\/gatk-launch"/"bcbio"/`
+vep_reference=$(readlink -f `which vep`| sed s/"\/vep"//)
+
+
+unset PERL5LIB && vep --vcf -o stdout \
+    -i $vcf --fork 5 --species homo_sapiens --no_stats --cache --offline --dir ${reference}/vep --symbol --numbers --biotype --total_length \
     --canonical --gene_phenotype --ccds --uniprot --domains --regulatory --protein --tsl --appris --af --max_af --af_1kg --af_esp --af_gnomad --pubmed --variant_class \
     --allele_number \
-    --fasta /hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa.gz \
-    --plugin LoF,human_ancestor_fa:/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/genomes/Hsapiens/GRCh37/variation/human_ancestor.fa.gz,\
-    loftee_path:/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/share/ensembl-vep-91.3-1 \
+    --fasta ${reference}/seq/GRCh37.fa.gz \
+    --plugin LoF,human_ancestor_fa:${reference}/variation/human_ancestor.fa.gz,\
+    loftee_path:$vep_reference \
     --plugin MaxEntScan,/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/share/maxentscan-0_2004.04.21-0 \
     --plugin SpliceRegion --sift b --polyphen b --hgvs --shift_hgvs 1 --merged \
     | sed '/^#/! s/;;/;/g' | bgzip -c > $bname.vepeffects.vcf.gz