filter_variants {seqCAT} | R Documentation |
Filter variants on several criteria.
filter_variants(data, min_depth = 10, filter_vc = FALSE, filter_mt = FALSE, filter_ns = FALSE)
data |
The dataframe containing the variant data to be filtered. |
min_depth |
Threshold for variant depth (integer). |
filter_vc |
Filter variants not passing filtering criteria (boolean). |
filter_mt |
Filter mitochondrial variants (boolean). |
filter_ns |
Filter non-standard chromosomes (boolean). |
This is a function for filtering SNV profiles on several criteria: sequencing depth, variant caller-specific filtering, mitochondrial variants and variants in non-standard chromosomes. Only filters by sequencing depth by default.
A data frame containing the filtered variants.
# Load test comparisons data(test_profile_1) # Filter variants filtered <- filter_variants(test_profile_1, min_depth = 15)