Skip to content

Latest commit

 

History

History
55 lines (48 loc) · 3.3 KB

VcfAnnotateConsequence.md

File metadata and controls

55 lines (48 loc) · 3.3 KB
Raw

VcfAnnotateConsequence tool help

VcfAnnotateConsequence (2024_08-110-g317f43b9)

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-112/gff3/homo_sapiens/Homo_sapiens.GRCh38.112.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 as 'GENCODE basic' for Ensembl and not with RefSeq/BestRefSeq origin for Refseq.
                           Default value: 'false'
  -skip_not_hgnc           Skip genes that do not have a HGNC identifier.
                           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'
  -source <enum>           GFF source.
                           Default value: 'ensembl'
                           Valid: 'ensembl,refseq'
  -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'.
  --settings [file]        Settings override file (no other settings files are used).

VcfAnnotateConsequence changelog

VcfAnnotateConsequence 2024_08-110-g317f43b9

2024-07-26 Added support for RefSeq GFF format (source parameter).
2022-07-07 Change to event-driven multithreaded implementation.

back to ngs-bits