This workflow provides the full power of bcftools view to subset, subsample, and filter VCF files.
All input files are referenced with either gs:// or drs:// URIs.
| parameter | required | default | description |
|---|---|---|---|
input_vcf |
required | Input VCF file. | |
input_vcf_index |
optional | VCF index file. If omitted, an index is created during execution. Instructions for creating index files are here. | |
samples |
optional | File of samples to be included in the output VCF. There should one sample per line. Additional information is here. | |
regions |
optional | File of regions to be included in the output VCF. The file should contain tab separated columns of chromosome (e.g. 'chr15'), start position, and optionally end position. Additional information is here. | |
view_options |
optional | -Oz |
Additional parameters to pass to the bcftools view command. If modified, view_options should typically include -Oz to produce a gzipped output VCF. |
filters |
optional | Filter arguments to pass into bcftools view. Filters will be applied in a separate, subsequent, call to bcftools view. |
|
output_filename |
optional | output.vcf.gz |
Name of the output vcf file. |
cpu |
optional | 8 |
Number of CPU cores. |
memory |
optional | 64 |
Amount of RAM in GB |
preemptible |
optional | 0 |
Whether to use preemptible instances, which are cheaper but my be revoked during execution. |