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Restore GERP annotations #206

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Restore GERP annotations #206

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821fe75
Restore GERP to VEP annotations
alkc Jun 26, 2024
d71354e
Update GERP CSQ hash key
alkc Jun 27, 2024
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2 changes: 1 addition & 1 deletion bin/modify_vcf_scout.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -171,7 +171,7 @@
push @add_info_field,"GNOMADPOP_MAX=$max_pop";
}
## GERP
my $GERP = $doobi->{INFO}->{CSQ}->[0]->{GERP};
my $GERP = $doobi->{INFO}->{CSQ}->[0]->{"GERP++_RS"};
if ($GERP) {
push @add_info_field,"dbNSFP_GERP___RS=$GERP";
}
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2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -1903,7 +1903,7 @@ process annotate_vep {
--plugin CADD,$params.CADD \\
--plugin LoFtool \\
--plugin MaxEntScan,$params.MAXENTSCAN,SWA,NCSS \\
--plugin dbNSFP,$params.DBNSFP,transcript_match=1,REVEL_score,REVEL_rankscore \\
--plugin dbNSFP,$params.DBNSFP,transcript_match=1,REVEL_score,REVEL_rankscore,GERP++_RS \\
-custom $params.GNOMAD_EXOMES,gnomADe,vcf,exact,0,AF_popmax,AF,popmax \\
-custom $params.GNOMAD_GENOMES,gnomADg,vcf,exact,0,AF_popmax,AF,popmax \\
-custom $params.GNOMAD_MT,gnomAD_mt,vcf,exact,0,AF_hom,AF_het \\
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