Command Line Options
|
Option |
Required |
Description |
|---|---|---|
|
--build-hash-table |
Yes |
Set to true. If it is set to false the pipeline will not use its end-to-end mode, and it will stop at the generation of the 3 intermediate files. |
|
--ht-graph-vcf-list |
Yes |
Path to the text file containing the list of VCF files to be used to build the custom multigenome hash table |
|
--ht-reference |
Yes |
Path to the reference genome FASTA file. Note: support only for human genome builds CHM13, hg38, hg19 and hs37d5. |
|
--ht-graph-bed |
Yes |
Path to the graph bed file |
|
--ht-mask-bed |
Yes |
Path to the mask bed file |
|
--output-directory |
Yes |
Specify the directory where all related hash table files will be written |
The custom reference hash table pipeline will return an error if options --ht-alt-liftover or --ht-allow-mask-and-liftover are specified.
