Filter a vcf to remove low-depth variant calls
usage: depth-filter [-h] [--minimum_depth MINIMUM_DEPTH]
[--site-depth-field SITE_DEPTH_FIELD]
[--filter-field FILTER_FIELD]
input_vcf sample_names output_vcf
positional arguments:
input_vcf A VCF file with at least two samples (tumor and
normal) and readcount information
sample_names comma-separated list of samples to which depth filter
will be applied
output_vcf Path to write the output VCF file
optional arguments:
-h, --help show this help message and exit
--minimum_depth MINIMUM_DEPTH
minimum depth for a variant
--site-depth-field SITE_DEPTH_FIELD
field corresponding to site depth - default DP
--filter-field FILTER_FIELD
if variant doesn't have a given depth, then failing
variants will have this string added to their FILTER
field```