2. Optional arguments¶
mutanno [sub-command] [options]
- optional arguments:
- -h, --help
show this help message and exit
- -v, --version
show program’s version number and exit
sub-commands:
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pre-calculate |
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validate data format |
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quality metrics for VCF |
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web view |
2.1. Run annotation (annot)¶
- -h, --help
show this help message and exit
- -vcf
input VCF file
- -out
title of output file
- -outtype [vcf, json]
output file type
- -ds
data structure json file
- -sourcefile
data source file
- -genoinfo
add genotype info. in INFO field
- -hgvs
add hgvs
- -variant_class
add variant class
- -hg19
add hg19 coordinates
- -chain
chain file for liftover of hg19 coordinates
- -genetable
add gene table
- -blocksize
block size
- -split_multi_allelic_variant
split multi-allelic variants
- -clean_tag
remove previous annotation information
- -single_source_mode
single source mode
- -load_source_in_memory
loading data source in memory
- -sparse
for sparse variant position
- -log
log file
- -silence
do not print any log.
- -debug
turn on the debugging mode