Closed aryarm closed 4 years ago
Currently, you most provide the vcf_file config option even if you provide the snp_h5_dir config option when calling the WASP or counts pipeline. Make it so that the vcf_file config option isn't required if the snp_h5_dir is provided.
vcf_file
snp_h5_dir
unfortunately, this won't be possible because the original vcf is required in order for the counts pipeline to extract GQ scores from it
Currently, you most provide the
vcf_file
config option even if you provide thesnp_h5_dir
config option when calling the WASP or counts pipeline. Make it so that thevcf_file
config option isn't required if thesnp_h5_dir
is provided.