Hail

ConvertToHailMT

description

Convert a .vcf.bgz file to a Hail MatrixTable and copy it to a final gs:// URL.

Inputs

Required

• gvcf (File, required): The input .vcf.bgz file.
• tbi (File, required): The input .vcf.bgz.tbi file.

Optional

• ref_fai (String?): The reference genome FASTA index file. If not specified, the reference genome will be downloaded from the Hail website.
• ref_fasta (String?): The reference genome FASTA file. If not specified, the reference genome will be downloaded from the Hail website.
• runtime_attr_override (RuntimeAttr?): Override the default runtime attributes for this task.

Defaults

• prefix (String, default="out"): The prefix to use for the output MatrixTable.
• reference (String, default="GRCh38"): The reference genome to use. Currently only GRCh38 is supported.

Outputs

• mt_tar (File)
• completion_file (File)