diff --git a/README.md b/README.md index 8b173c9..4d3e1b8 100644 --- a/README.md +++ b/README.md @@ -16,12 +16,14 @@ pipeline. Currently, the following settings can be made: ```yaml read_cut_padding: # int, padding left and right of the conflict region -region_file: # str (path to a conflict file) -alternative_haplotype_vcf: # str (path to a vcf file with known SVs, e.g. -from the HGSVC) +# path to a conflict file +region_file: # str + +# path to a vcf file with known SVs, e.g. from the HGSVC +alternative_haplotype_vcf: # str # path to liftover directory (explained below) -liftover_root: # default to 'resources/references/liftover' +liftover_root: # str, defaults to 'resources/references/liftover' # Settings for the pairwise alignment pw_alignment: