Read Strelka variants
strelka.RdReads the variant calls from Strelka2 Small Variant Caller
Usage
read_strelka_somatic_snvs(
path,
sample_ids = "drop_first",
PASS_only = TRUE,
patient_id_pattern = "(?<=\\/)[:alnum:]*(?=\\.)",
chrom_convention = "UCSC",
verbose = TRUE
)Arguments
- path
Can be either:
path to a single file
vector of file paths, element names will be used as patient IDs
directory containing multiple Mutect .vcf files, patient IDs will be guessed from the file names (should follow convention: <patient_ID>.XXX.XXX.vcf)
- sample_ids
Either:
"drop_first"
"all"
ID(s) of the selected tumor samples.
Default: "drop_first"
- PASS_only
Keep FILTER == PASS variants only?
- patient_id_pattern
If path is a dir only: pattern for str_extract() that should be used to extract the patient_id from the filenames
- chrom_convention
UCSC/NCBI/keep
- verbose
Verbose?
Examples
library(readthis)
file1 <- system.file("extdata", "Strelka", "S1.somatic.snvs.vcf.gz", package = "readthis")
read_strelka_somatic_snvs(file1)
#> Scanning file to determine attributes.
#> File attributes:
#> meta lines: 53
#> header_line: 54
#> variant count: 12
#> column count: 11
#>
Meta line 53 read in.
#> All meta lines processed.
#> gt matrix initialized.
#> Character matrix gt created.
#> Character matrix gt rows: 12
#> Character matrix gt cols: 11
#> skip: 0
#> nrows: 12
#> row_num: 0
#>
Processed variant: 12
#> All variants processed
#> Extracting gt element DP
#> Extracting gt element FDP
#> Extracting gt element SDP
#> Extracting gt element SUBDP
#> Extracting gt element AU
#> Extracting gt element CU
#> Extracting gt element GU
#> Extracting gt element TU
#> readthis>Guessing sample_ids: TUMOR
#> # A tibble: 9 × 9
#> sample_id chrom pos ref alt ref_reads alt_reads VAF DP
#> <chr> <chr> <int> <chr> <chr> <int> <int> <dbl> <int>
#> 1 TUMOR chr1 1 T G 40 2 0.0476 1000
#> 2 TUMOR chr2 3 A T 27 3 0.1 554
#> 3 TUMOR chr3 5 C A 23 3 0.115 412
#> 4 TUMOR chr4 7 T C 39 10 0.204 932
#> 5 TUMOR chr5 8 A C 59 3 0.0484 945
#> 6 TUMOR chr6 9 C A 25 2 0.0741 500
#> 7 TUMOR chr7 10 A C 35 2 0.0541 870
#> 8 TUMOR chrX 11 A T 32 1 0.0303 893
#> 9 TUMOR chrY 12 T A 62 3 0.0462 740
file2 <- system.file("extdata", "Strelka", "S2.somatic.snvs.vcf.gz", package = "readthis")
files <- c(S1 = file1, S2 = file2)
read_strelka_somatic_snvs(files, verbose = FALSE)
#> # A tibble: 18 × 10
#> patient_id sample_id chrom pos ref alt ref_reads alt_reads VAF DP
#> <chr> <chr> <chr> <int> <chr> <chr> <int> <int> <dbl> <int>
#> 1 S1 TUMOR chr1 1 T G 40 2 0.0476 1000
#> 2 S1 TUMOR chr2 3 A T 27 3 0.1 554
#> 3 S1 TUMOR chr3 5 C A 23 3 0.115 412
#> 4 S1 TUMOR chr4 7 T C 39 10 0.204 932
#> 5 S1 TUMOR chr5 8 A C 59 3 0.0484 945
#> 6 S1 TUMOR chr6 9 C A 25 2 0.0741 500
#> 7 S1 TUMOR chr7 10 A C 35 2 0.0541 870
#> 8 S1 TUMOR chrX 11 A T 32 1 0.0303 893
#> 9 S1 TUMOR chrY 12 T A 62 3 0.0462 740
#> 10 S2 TUMOR chr1 1 T G 40 2 0.0476 1000
#> 11 S2 TUMOR chr2 3 A T 27 3 0.1 554
#> 12 S2 TUMOR chr3 5 C A 23 3 0.115 412
#> 13 S2 TUMOR chr4 7 T C 39 10 0.204 932
#> 14 S2 TUMOR chr5 8 A C 59 3 0.0484 945
#> 15 S2 TUMOR chr6 9 C A 25 2 0.0741 500
#> 16 S2 TUMOR chr7 10 A C 35 2 0.0541 870
#> 17 S2 TUMOR chrX 11 A T 32 1 0.0303 893
#> 18 S2 TUMOR chrY 12 T A 62 3 0.0462 740
dir <- system.file("extdata", "Strelka", package = "readthis")
read_strelka_somatic_snvs(dir)
#> Scanning file to determine attributes.
#> File attributes:
#> meta lines: 53
#> header_line: 54
#> variant count: 12
#> column count: 11
#>
Meta line 53 read in.
#> All meta lines processed.
#> gt matrix initialized.
#> Character matrix gt created.
#> Character matrix gt rows: 12
#> Character matrix gt cols: 11
#> skip: 0
#> nrows: 12
#> row_num: 0
#>
Processed variant: 12
#> All variants processed
#> Extracting gt element DP
#> Extracting gt element FDP
#> Extracting gt element SDP
#> Extracting gt element SUBDP
#> Extracting gt element AU
#> Extracting gt element CU
#> Extracting gt element GU
#> Extracting gt element TU
#> readthis>Guessing sample_ids: TUMOR
#> Scanning file to determine attributes.
#> File attributes:
#> meta lines: 53
#> header_line: 54
#> variant count: 12
#> column count: 11
#>
Meta line 53 read in.
#> All meta lines processed.
#> gt matrix initialized.
#> Character matrix gt created.
#> Character matrix gt rows: 12
#> Character matrix gt cols: 11
#> skip: 0
#> nrows: 12
#> row_num: 0
#>
Processed variant: 12
#> All variants processed
#> Extracting gt element DP
#> Extracting gt element FDP
#> Extracting gt element SDP
#> Extracting gt element SUBDP
#> Extracting gt element AU
#> Extracting gt element CU
#> Extracting gt element GU
#> Extracting gt element TU
#> readthis>Guessing sample_ids: TUMOR
#> # A tibble: 18 × 10
#> patient_id sample_id chrom pos ref alt ref_reads alt_reads VAF DP
#> <chr> <chr> <chr> <int> <chr> <chr> <int> <int> <dbl> <int>
#> 1 S1 TUMOR chr1 1 T G 40 2 0.0476 1000
#> 2 S1 TUMOR chr2 3 A T 27 3 0.1 554
#> 3 S1 TUMOR chr3 5 C A 23 3 0.115 412
#> 4 S1 TUMOR chr4 7 T C 39 10 0.204 932
#> 5 S1 TUMOR chr5 8 A C 59 3 0.0484 945
#> 6 S1 TUMOR chr6 9 C A 25 2 0.0741 500
#> 7 S1 TUMOR chr7 10 A C 35 2 0.0541 870
#> 8 S1 TUMOR chrX 11 A T 32 1 0.0303 893
#> 9 S1 TUMOR chrY 12 T A 62 3 0.0462 740
#> 10 S2 TUMOR chr1 1 T G 40 2 0.0476 1000
#> 11 S2 TUMOR chr2 3 A T 27 3 0.1 554
#> 12 S2 TUMOR chr3 5 C A 23 3 0.115 412
#> 13 S2 TUMOR chr4 7 T C 39 10 0.204 932
#> 14 S2 TUMOR chr5 8 A C 59 3 0.0484 945
#> 15 S2 TUMOR chr6 9 C A 25 2 0.0741 500
#> 16 S2 TUMOR chr7 10 A C 35 2 0.0541 870
#> 17 S2 TUMOR chrX 11 A T 32 1 0.0303 893
#> 18 S2 TUMOR chrY 12 T A 62 3 0.0462 740