Reads the TMB_Trace.tsv file output from the TSO500 workflow.
Examples
x <- system.file("extdata/tso/sample705_TMB_Trace.tsv", package = "dracarys")
tso_tmbt_read(x)
#> # A tibble: 1,639 × 20
#> Chromosome Position RefCall AltCall VAF Depth CytoBand GeneName
#> <chr> <dbl> <chr> <chr> <dbl> <dbl> <chr> <chr>
#> 1 chr1 2488153 A G 0.559 93 1p36.32 LOC100133445:TNFRS…
#> 2 chr1 4367323 G A 1 55 1p36.32 NA
#> 3 chr1 11205058 C T 1 52 1p36.22 MTOR:MTOR-AS1
#> 4 chr1 11288758 G A 1 75 1p36.22 MTOR
#> 5 chr1 11301714 A G 1 82 1p36.22 MTOR
#> 6 chr1 18957546 G A 0.573 75 1p36.13 PAX7
#> 7 chr1 19027239 A G 0.581 117 1p36.13 PAX7
#> 8 chr1 19071752 T C 1 107 1p36.13 PAX7
#> 9 chr1 19071759 G T 0.0182 110 1p36.13 PAX7
#> 10 chr1 19072926 A G 1 79 1p36.13 PAX7
#> # ℹ 1,629 more rows
#> # ℹ 12 more variables: VariantType <chr>, CosmicIDs <chr>,
#> # MaxCosmicCount <dbl>, AlleleCountsGnomadExome <dbl>,
#> # AlleleCountsGnomadGenome <dbl>, AlleleCounts1000Genomes <dbl>,
#> # MaxDatabaseAlleleCounts <dbl>, GermlineFilterDatabase <chr>,
#> # GermlineFilterProxi <chr>, CodingVariant <chr>, Nonsynonymous <chr>,
#> # IncludedInTMBNumerator <chr>