update vep path

Author: Cao

somaticwrapper.pl

@@ -230,8 +230,8 @@
 my $samtools="/storage1/fs1/songcao/Active/Software/samtools/1.2/bin";
 my $varscan="/storage1/fs1/songcao/Active/Software/varscan/2.3.8.ndown";
 my $bamreadcount="/storage1/fs1/songcao/Active/Software/bam-readcount/0.7.4/bam-readcount";
-my $vepannot="/storage1/fs1/songcao/Active/Database/hg38_database/vep/ensembl-tools-release-85/scripts/variant_effect_predictor/variant_effect_predictor.v102.pl";
-my $vepannot="/storage1/fs1/songcao/Active/Git/ensembl-vep/vep";
+#my $vepannot="/storage1/fs1/songcao/Active/Database/hg38_database/vep/ensembl-tools-release-85/scripts/variant_effect_predictor/variant_effect_predictor.v102.pl";
+my $vepannot="/storage1/fs1/dinglab/Active/Projects/scao/gitshared/ensembl-vep/vep";
 
 #my $vepcache="/storage1/fs1/songcao/Active/Database/hg38_database/vep/v85";
 

vcf2maf.pl

@@ -20,7 +20,10 @@
 my $perl_bin = $Config{perlpath};
 
 # Find out if samtools and tabix are properly installed, and warn the user if it's not
-my ( $samtools ) = map{chomp; $_}`which samtools`;
+#my ( $samtools ) = map{chomp; $_}`which samtools`;
+
+my $samtools = "/storage1/fs1/songcao/Active/Software/anaconda3/bin/samtools"; 
+
 ( $samtools and -e $samtools ) or die "ERROR: Please install samtools, and make sure it's in your PATH\n";
 my ( $tabix ) = map{chomp; $_}`which tabix`;
 ( $tabix and -e $tabix ) or die "ERROR: Please install tabix, and make sure it's in your PATH\n";

work_log_run_mild_v102

@@ -3,4 +3,3 @@ perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildvep102 --log /sc
 perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildvep102 --log /scratch1/fs1/dinglab/scao/sw/mildvep102.log --ref  /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg  /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --step 12 --sre 1
 
 perl somaticwrapper.pl --rdir /scratch1/fs1/dinglab/scao/sw/mildvep102 --log /scratch1/fs1/dinglab/scao/sw/mildvep102.log --ref  /storage1/fs1/songcao/Active/Database/hg38_database/GRCh38.d1.vd1/GRCh38.d1.vd1.fa --q general --smg  /storage1/fs1/songcao/Active/Database/smg_database/smg.lung.tsv --users songcao --groupname SomaticWXS --sre 1 --step 13 --sre 1
-