diff --git a/docs/vep_maf_readme.txt b/docs/vep_maf_readme.txt index a99433d..f7a9498 100644 --- a/docs/vep_maf_readme.txt +++ b/docs/vep_maf_readme.txt @@ -124,7 +124,7 @@ These are some other columns to help shortlist variants worth looking into: 73. PolyPhen - the PolyPhen prediction and/or score. 109. FILTER - False-positive filtering status, copied from the input MAF/VCF. An additional filter named common_variant is also appended, if allele count across at least one ExAC subpopulation - is >16 (this default cutoff can be changed when running vcf2maf). So if you're handling + is >10 (this default cutoff can be changed when running vcf2maf). So if you're handling somatic variants, the common_variant tag means this is likely a false-positive. It is less likely to be a legit somatic variant at a site that ExAC classifies as germline or artifact. 123. ExAC_FILTER - FILTER tags copied from the ExAC VCF. Differentiates between what ExAC classifies diff --git a/maf2maf.pl b/maf2maf.pl index 73fe6c5..d43681a 100644 --- a/maf2maf.pl +++ b/maf2maf.pl @@ -17,7 +17,7 @@ my ( $nrm_depth_col, $nrm_rad_col, $nrm_vad_col ) = qw( n_depth n_ref_count n_alt_count ); my ( $vep_path, $vep_data, $vep_forks ) = ( "$ENV{HOME}/vep", "$ENV{HOME}/.vep", 4 ); my ( $ref_fasta, $filter_vcf ) = ( "$ENV{HOME}/.vep/homo_sapiens/86_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz", "$ENV{HOME}/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz" ); -my ( $species, $ncbi_build, $cache_version, $maf_center, $min_hom_vaf, $max_filter_ac ) = ( "homo_sapiens", "GRCh37", "", ".", 0.7, 11 ); +my ( $species, $ncbi_build, $cache_version, $maf_center, $min_hom_vaf, $max_filter_ac ) = ( "homo_sapiens", "GRCh37", "", ".", 0.7, 10 ); my $perl_bin = $Config{perlpath}; # Columns that can be safely borrowed from the input MAF @@ -370,7 +370,7 @@ =head1 OPTIONS --vep-data VEP's base cache/plugin directory [~/.vep] --vep-forks Number of forked processes to use when running VEP [4] --filter-vcf The non-TCGA VCF from exac.broadinstitute.org [~/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz] - --max-filter-ac Use tag common_variant if the filter-vcf reports a subpopulation AC higher than this [11] + --max-filter-ac Use tag common_variant if the filter-vcf reports a subpopulation AC higher than this [10] --species Ensembl-friendly name of species (e.g. mus_musculus for mouse) [homo_sapiens] --ncbi-build NCBI reference assembly of variants in MAF (e.g. GRCm38 for mouse) [GRCh37] --cache-version Version of offline cache to use with VEP (e.g. 75, 82, 86) [Default: Installed version] diff --git a/vcf2maf.pl b/vcf2maf.pl index ee3c6fd..c3fc45f 100644 --- a/vcf2maf.pl +++ b/vcf2maf.pl @@ -14,7 +14,7 @@ my ( $tumor_id, $normal_id ) = ( "TUMOR", "NORMAL" ); my ( $vep_path, $vep_data, $vep_forks ) = ( "$ENV{HOME}/vep", "$ENV{HOME}/.vep", 4 ); my ( $ref_fasta, $filter_vcf ) = ( "$ENV{HOME}/.vep/homo_sapiens/86_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz", "$ENV{HOME}/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz" ); -my ( $species, $ncbi_build, $cache_version, $maf_center, $retain_info, $min_hom_vaf, $max_filter_ac ) = ( "homo_sapiens", "GRCh37", "", ".", "", 0.7, 11 ); +my ( $species, $ncbi_build, $cache_version, $maf_center, $retain_info, $min_hom_vaf, $max_filter_ac ) = ( "homo_sapiens", "GRCh37", "", ".", "", 0.7, 10 ); my $perl_bin = $Config{perlpath}; # Find out if samtools and tabix are properly installed, and warn the user if it's not @@ -935,7 +935,7 @@ =head1 OPTIONS --vep-forks Number of forked processes to use when running VEP [4] --ref-fasta Reference FASTA file [~/.vep/homo_sapiens/86_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz] --filter-vcf The non-TCGA VCF from exac.broadinstitute.org [~/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz] - --max-filter-ac Use tag common_variant if the filter-vcf reports a subpopulation AC higher than this [11] + --max-filter-ac Use tag common_variant if the filter-vcf reports a subpopulation AC higher than this [10] --species Ensembl-friendly name of species (e.g. mus_musculus for mouse) [homo_sapiens] --ncbi-build NCBI reference assembly of variants MAF (e.g. GRCm38 for mouse) [GRCh37] --cache-version Version of offline cache to use with VEP (e.g. 75, 82, 86) [Default: Installed version]