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Remove deprecated VEP 110 argument #350

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merged 1 commit into from
May 30, 2024
Merged

Remove deprecated VEP 110 argument #350

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2 changes: 1 addition & 1 deletion maf2maf.pl
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,7 @@
# Add options that only work on human variants
if( $species eq "homo_sapiens" ) {
# Slight change in these arguments if using the newer VEP
$vep_cmd .= " --polyphen b " . ( $vep_script =~ m/vep$/ ? "--af --af_1kg --af_esp --af_gnomad" : "--gmaf --maf_1kg --maf_esp" );
$vep_cmd .= " --polyphen b " . ( $vep_script =~ m/vep$/ ? "--af --af_1kg --af_gnomad" : "--gmaf --maf_1kg --maf_esp" );
}
# Add options that work for most species, except a few
$vep_cmd .= " --regulatory" unless( $species eq "canis_familiaris" );
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2 changes: 1 addition & 1 deletion vcf2maf.pl
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Expand Up @@ -485,7 +485,7 @@ sub GetBiotypePriority {
if( $species eq "homo_sapiens" ) {
# Slight change in options if in offline mode, or if using the newer VEP
$vep_cmd .= " --polyphen b" . ( $vep_script =~ m/vep$/ ? " --af" : " --gmaf" );
$vep_cmd .= ( $vep_script =~ m/vep$/ ? " --af_1kg --af_esp --af_gnomad" : " --maf_1kg --maf_esp" ) unless( $online );
$vep_cmd .= ( $vep_script =~ m/vep$/ ? " --af_1kg --af_gnomad" : " --maf_1kg --maf_esp" ) unless( $online );
}
# Do not use the --regulatory option in situations where we know it will break
$vep_cmd .= " --regulatory" unless( $species eq "canis_familiaris" or $online );
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