allow input as h5 files

aryarm / as_analysis

A complete Snakemake pipeline for detecting allele specific expression in RNA-seq

MIT License

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allow input as h5 files #54

Closed aryarm closed 4 years ago

aryarm commented 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.

aryarm commented 4 years ago

unfortunately, this won't be possible because the original vcf is required in order for the counts pipeline to extract GQ scores from it