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VcfAnnotateMaxEntScan tool help

VcfAnnotateMaxEntScan (2024_08-110-g317f43b9)

Annotates a VCF file with MaxEntScan scores.

Mandatory parameters:
  -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.

Optional parameters:
  -out <file>        Output VCF file containing the MaxEntScan scores in the INFO column. If unset, writes to STDOUT.
                     Default value: ''
  -in <file>         Input VCF file. If unset, reads from STDIN.
                     Default value: ''
  -swa               Enables sliding window approach, i.e. predictions of de-novo acceptor/donor sites.
                     Default value: 'false'
  -all               If set, all transcripts are used for annotation (the default is to skip transcripts not labeled with the 'GENCODE basic' tag).
                     Default value: 'false'
  -tag <string>      Info entry name used for native splice site scores.
                     Default value: 'MES'
  -tag_swa <string>  Info entry name used for SWA scores.
                     Default value: 'MES_SWA'
  -decimals <int>    Number of decimals of output scores.
                     Default value: '2'
  -min_score <float> Minimum score to report.
                     Default value: '-1000'
  -threads <int>     The number of threads used to process VCF line chunk.
                     Default value: '1'
  -block_size <int>  Number of VCF lines processed in one chunk.
                     Default value: '10000'
  -prefetch <int>    Maximum number of chunks that may be pre-fetched into memory.
                     Default value: '64'
  -ref <file>        Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
                     Default value: ''
  -debug             Enables debug output (use only with one thread).
                     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).

VcfAnnotateMaxEntScan changelog

VcfAnnotateMaxEntScan 2024_08-110-g317f43b9

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