9.6 Genome Parameters
| Parameter | Description | Default |
|---|---|---|
--chr chr1,chr2,chr3 |
List of chromosomes to use | all |
--chr chrs.txt |
File with chromosome and corresponding ploidy to use | all |
--limitChr |
Limit chromosomes up to given name | all |
--regions regions.bed |
Only use these positions | use all positions |
--mask mask.bed |
Mask these positions | don’t mask |
--alleles alleles.txt |
Only use these positions with given ref- and alt- bases | don’t use alleles |
Example alleles file
chr pos ref alt
chr1 1000 A C
chr1 1001 T G
chr2 3000 C NThe alt column is not always used, depending on use-case