vcf-info-annotator A tool that will add data from a tab-delimited file to any user-specified field in the VCF INFO column. vcf-genotype-annotator A tool to add a new sample to an existing VCF file. vep-annotation-reporter A tool to create a tab-delimited (TSV) file of variants in a...
ERROR: Failed to run the VEP annotator! #334 opened Oct 17, 2022 by EsterAH 2 Add options for RefSeq and Merged caches when converting to MAF #333 opened Oct 12, 2022 by bkohrn Empty 't_depth' 't_ref_count' 't_alt_count' #332 opened Sep 9, 2022 by QingruXu44004 1 ...
importhtsjdk.variant.vcf.VCFFormatHeaderLine;//导入依赖的package包/类@Overridepublicvoidinitialize(finalAnnotatorCompatible walker,finalGenomeLocParser parser,finalSet<VCFHeaderLine> headerLines){booleanhasSBBSannotation =false;for(finalVCFHeaderLine line : headerLines) {if(lineinstanceofVCFFormatHeaderLine) ...
for ( final GenotypeAnnotation annotation : requestedGenotypeAnnotations ) descriptions.addAll(annotation.getDescriptions()); for ( final String db : variantOverlapAnnotator.getOverlapNames() ) { if ( VCFStandardHeaderLines.getInfoLine(db, false) != null ) descriptions.add(VCFStandardHeaderLines.getIn...
system( $vep_cmd ) == 0 or die "\nERROR: Failed to run the VEP annotator! Command: $vep_cmd\n"; ( -s $vep_anno ) or warn "WARNING: VEP-annotated VCF file is missing or empty: $vep_anno\n"; } # Load the tumor-normal pairs from the TSV created by maf2vcf my $tsv...
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##GATKCommandLine=<ID=CombineVariants,Version=2.7-63-gc434461,Date="Mon Oct 14 15:08:05...
importhtsjdk.variant.vcf.VCFHeaderLine;//導入依賴的package包/類@Overridepublicvoidinitialize(finalAnnotatorCompatible walker,finalGenomeLocParser parser,finalSet<VCFHeaderLine> headerLines){booleanhasSBBSannotation =false;for(finalVCFHeaderLineline : headerLines) {if(lineinstanceofVCFFormatHeaderLine) {final...
If you don't have VEP installed, thenfollow this gist. Of the many annotators out there, VEP is preferred for its large team of active coders, and its CLIA-compliantHGVS formats. After installing VEP, test outvcf2maflike this: perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf...
Search or jump to... Search code, repositories, users, issues, pull requests... Provide feedback We read every piece of feedback, and take your input very seriously. Include my email address so I can be contacted Cancel Submit feedback Saved searches Use saved searches to filter your...
logger.info("changing eigen file prefix from :"+this.annotator.getTabixPrefix()+" to "+this.tabixPrefix);this.annotator.setTabixFilePrefix(this.tabixPrefix); }finalVCFHeader header1=super.getVcfHeader();finalVCFHeader h2 =newVCFHeader(header1);for(finalVCFInfoHeaderLinevihl:this.annotator.get...