Tighter default max-filter-ac of 10

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

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]

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]