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Commit cb067661 authored by Brandi Cantarel's avatar Brandi Cantarel
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update cnvkit

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variants/annotvcf.sh
+ 1
− 1
View file @ cb067661
......@@ -36,7 +36,7 @@ then
bcftools annotate -Oz -a ${index_path}/gnomad.txt.gz -h ${index_path}/gnomad.header -c CHROM,POS,REF,ALT,GNOMAD_HOM,GNOMAD_AF,AF_POPMAX -o ${pair_id}.gnomad.vcf.gz ${unionvcf}
tabix ${pair_id}.gnomad.vcf.gz
bcftools annotate -Oz -a ${index_path}/repeat_regions.bed.gz -o ${pair_id}.repeat.vcf.gz --columns CHROM,FROM,TO,RepeatType -h /project/shared/bicf_workflow_ref/RepeatType.header ${pair_id}.gnomad.vcf.gz
java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.repeat.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar annotate -id ${index_path}/dbSnp.vcf.gz - | java -jar $SNPEFF_HOME/SnpSift.jar annotate -info CLNSIG,CLNDSDB,CLNDSDBID,CLNDBN,CLNREVSTAT,CLNACC ${index_path}/clinvar.vcf.gz - | java -jar $SNPEFF_HOME/SnpSift.jar annotate -info CNT ${index_path}/cosmic.vcf.gz - | java -Xmx10g -jar $SNPEFF_HOME/SnpSift.jar dbnsfp -v -db ${index_path}/dbNSFP.txt.gz - | bgzip > ${pair_id}.annot.vcf.gz
java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-downstream -no-upstream -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.repeat.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar annotate -id ${index_path}/dbSnp.vcf.gz - | java -jar $SNPEFF_HOME/SnpSift.jar annotate -info CLNSIG,CLNDSDB,CLNDSDBID,CLNDBN,CLNREVSTAT,CLNACC ${index_path}/clinvar.vcf.gz - | java -jar $SNPEFF_HOME/SnpSift.jar annotate -info CNT ${index_path}/cosmic.vcf.gz - | java -Xmx10g -jar $SNPEFF_HOME/SnpSift.jar dbnsfp -v -db ${index_path}/dbNSFP.txt.gz - | bgzip > ${pair_id}.annot.vcf.gz
tabix ${pair_id}.annot.vcf.gz
else
if [[ $index_path == '/project/shared/bicf_workflow_ref/GRCm38' ]]
......
variants/filter_cnvkit.pl
+ 26
− 10
View file @ cb067661
......@@ -60,11 +60,19 @@ while (my $line = <CNR>) {
my ($chr,$start,$end,$geneids,$log2,$depth,$weight) = split(/\t/,$line);
my $key = $chr.":".$start."-".$end;
my %genes;
my @ids = split(/;|,/,$geneids);
foreach my $gid (@ids) {
my ($key,$value) = split(/=/,$gid);
if ($key eq 'ensembl_gn' || $key eq 'identifier') {
$genes{$value} = 1 if $keep{$value};
if ($geneids =~ m/ensembl_gn/g) {
my @ids = split(/;|,/,$geneids);
foreach my $gid (@ids) {
my ($key,$value) = split(/=/,$gid);
if ($key eq 'ensembl_gn' || $key eq 'identifier') {
$genes{$value} = 1 if $keep{$value};
}
}
}else {
my @ids = split(/,/,$geneids);
foreach my $gid (@ids) {
my ($gene,$trxid,$exonnum,$strand) = split(/\|/,$gid);
$genes{$gene} = 1 if $keep{$gene};
}
}
foreach $gene (keys %genes) {
......@@ -81,11 +89,19 @@ while (my $line = <IN>) {
next if ($chr eq 'chrX' && $cn == 1);
my $key = $chr.":".$start."-".$end;
my %genes;
my @ids = split(/;|,/,$geneids);
foreach my $gid (@ids) {
my ($key,$value) = split(/=/,$gid);
if ($key eq 'ensembl_gn' || $key eq 'identifier') {
$genes{$value} = 1 if $keep{$value};
if ($geneids =~ m/ensembl_gn/g) {
my @ids = split(/;|,/,$geneids);
foreach my $gid (@ids) {
my ($key,$value) = split(/=/,$gid);
if ($key eq 'ensembl_gn' || $key eq 'identifier') {
$genes{$value} = 1 if $keep{$value};
}
}
}else {
my @ids = split(/,/,$geneids);
foreach my $gid (@ids) {
my ($gene,$trxid,$exonnum,$strand) = split(/\|/,$gid);
$genes{$gene} = 1 if $keep{$gene};
}
}
my $len = sprintf("%.1f",($end-$start)/1000);
......
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