VcfAnnotateConsequence (2022_11-75-gf99b2041)
Adds transcript-specific consequence predictions to a VCF file.
Variants are normalized accoring to the HGVS 3' rule to assess the effect, i.e. they are moved as far as possible in translation direction.
Note: HGVS consequence calcualtion is only done if the variant is fully inside the transcript region.
Mandatory parameters:
-in <file> Input VCF file to annotate.
-gff <file> Ensembl-style GFF file with transcripts, e.g. from https://ftp.ensembl.org/pub/release-107/gff3/homo_sapiens/Homo_sapiens.GRCh38.107.gff3.gz.
-out <file> Output VCF file annotated with predicted consequences for each variant.
Optional parameters:
-ref <file> Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
Default value: ''
-threads <int> The number of threads used to read, process and write files.
Default value: '1'
-block_size <int> Number of lines processed in one chunk.
Default value: '5000'
-prefetch <int> Maximum number of blocks that may be pre-fetched into memory.
Default value: '64'
-all If set, all transcripts are imported (the default is to skip transcripts not labeled with the 'GENCODE basic' tag).
Default value: 'false'
-tag <string> Tag that is used for the consequence annotation.
Default value: 'CSQ'
-max_dist_to_trans <int> Maximum distance between variant and transcript.
Default value: '5000'
-splice_region_ex <int> Number of bases at exon boundaries that are considered to be part of the splice region.
Default value: '3'
-splice_region_in5 <int> Number of bases at intron boundaries (5') that are considered to be part of the splice region.
Default value: '20'
-splice_region_in3 <int> Number of bases at intron boundaries (3') that are considered to be part of the splice region.
Default value: '20'
-debug Enable debug output
Default value: 'false'
Special parameters:
--help Shows this help and exits.
--version Prints version and exits.
--changelog Prints changeloge and exits.
--tdx Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
VcfAnnotateConsequence 2022_11-75-gf99b2041
2022-07-07 Change to event-driven multithreaded implementation.