From 903f1fd2a1d30788728f3ac200d7a50a92c53aff Mon Sep 17 00:00:00 2001
From: "naumenko.sa" <evolgenomicslab@gmail.com>
Date: Tue, 10 Sep 2024 15:39:04 -0400
Subject: [PATCH] test

---
 cram2bam.sh |  2 ++
 cre.vep.sh  | 51 ---------------------------------------------------
 2 files changed, 2 insertions(+), 51 deletions(-)
 delete mode 100755 cre.vep.sh

diff --git a/cram2bam.sh b/cram2bam.sh
index 7201351..0d570b1 100644
--- a/cram2bam.sh
+++ b/cram2bam.sh
@@ -5,6 +5,8 @@
 #PBS -d .
 #PBS -l vmem=20g,mem=20g
 
+# test
+
 module load java
 
 cramtools bam -I $cram -O $bam -b -R $ref
diff --git a/cre.vep.sh b/cre.vep.sh
deleted file mode 100755
index 03c3148..0000000
--- a/cre.vep.sh
+++ /dev/null
@@ -1,51 +0,0 @@
-#/bin/bash
-
-# gemini.vcf2vep annotates vcf with vep before loading to gemini database
-# based on  bcbio.log
-# uses hgvs notation and no --pick = all effects for a gene
-# 10h walltime is not enough for genomes or big multisample vcfs
-
-#PBS -l walltime=23:00:00,nodes=1:ppn=1
-#PBS -joe .
-#PBS -d .
-#PBS -l vmem=30g,mem=30g
-
-if [ -z $vcf ]
-then
-    vcf=$1
-fi
-
-if [ -z $threads ]
-then
-    threads=5
-fi
-
-. /hpf/largeprojects/ccmbio/naumenko/tools/bcbio_1.1.5/.profile115
-
-bname=`basename $vcf .vcf.gz`
-
-#find reference
-reference=`readlink -f $(which bcbio_nextgen.py) | sed s/"anaconda\/bin\/bcbio_nextgen.py"/"genomes\/Hsapiens\/GRCh37"/`
-vep_reference=`readlink -f $(which vep) | sed s/"\/vep"//`
-
-echo "Threads:" $threads
-
-#unset PERL5LIB && vep --vcf -o stdout \
-#    -i $vcf --fork $threads --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 ${reference}/seq/GRCh37.fa.gz \
-#    --plugin LoF,human_ancestor_fa:${reference}/variation/human_ancestor.fa.gz,loftee_path:$vep_reference \
-#    --plugin MaxEntScan,/hpf/largeprojects/ccmbio/naumenko/tools/bcbio/anaconda/share/maxentscan-0_2004.04.21-1 \
-#    --plugin SpliceRegion --sift b --polyphen b --hgvs --shift_hgvs 1 --merged \
-#    | sed '/^#/! s/;;/;/g' | bgzip -c > $bname.vepeffects.vcf.gz
-
-unset PERL5LIB && vep --vcf -o stdout \
-    -i $vcf --fork $threads --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 ${reference}/seq/GRCh37.fa.gz \
-    --plugin LoF,human_ancestor_fa:${reference}/human_ancestor.fa.gz,loftee_path:$vep_reference \
-    --plugin MaxEntScan,/hpf/largeprojects/ccmbio/naumenko/tools/bcbio_1.1.5/anaconda/share/maxentscan-0_2004.04.21-1 \
-    --plugin SpliceRegion --sift b --polyphen b --hgvsg --hgvs --shift_hgvs 1 --merged \
-    | sed '/^#/! s/;;/;/g' | bgzip -c > $bname.vepeffects.vcf.gz