From d459a9cd6781b5463c71300787a237640486c80f Mon Sep 17 00:00:00 2001 From: Cyriac Kandoth Date: Fri, 22 May 2015 15:29:53 -0400 Subject: [PATCH] Enable shift-hgvs for VEP --- vcf2maf.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vcf2maf.pl b/vcf2maf.pl index 3368cc0..d56957a 100644 --- a/vcf2maf.pl +++ b/vcf2maf.pl @@ -252,7 +252,7 @@ sub GetBiotypePriority { ( -s $ref_fasta ) or die "ERROR: Reference FASTA not found: $ref_fasta\n"; # Contruct VEP command using some default options and run it - my $vep_cmd = "$perl_bin $vep_path/variant_effect_predictor.pl --quiet --offline --no_stats --everything --check_existing --total_length --allele_number --no_escape --gencode_basic --xref_refseq --assembly $ncbi_build --dir $vep_data --fasta $ref_fasta --vcf --input_file $input_vcf --output_file $vep_anno"; + my $vep_cmd = "$perl_bin $vep_path/variant_effect_predictor.pl --quiet --offline --no_stats --everything --shift_hgvs --check_existing --total_length --allele_number --no_escape --gencode_basic --xref_refseq --assembly $ncbi_build --dir $vep_data --fasta $ref_fasta --vcf --input_file $input_vcf --output_file $vep_anno"; $vep_cmd .= " --fork $vep_forks" if( $vep_forks > 1 ); system( $vep_cmd ) == 0 or die "\nERROR: Failed to run the VEP annotator!\nCommand: $vep_cmd\n";