gtMarkers | R Documentation |
The function will generate tsv files '<tumor/normal>_nucleotide_counts.tsv' that can be used for downstream analysis. Note that the function will process ~900K loci from Affymetrix Genome-Wide Human SNP 6.0 Array. The process can be sped up by increasing 'nthreads' which will launch each chromosome on a separate thread. Currently hg19 and hg38 are supported. Files need to be further processed with prepAscat
for tumor-normal pair, or prepAscat_t
for tumor only samples.
gtMarkers(
t_bam = NULL,
n_bam = NULL,
build = "hg19",
prefix = NULL,
add = TRUE,
mapq = 10,
sam_flag = 1024,
loci = NULL,
fa = NULL,
op = NULL,
zerobased = FALSE,
nthreads = 4,
verbose = TRUE
)
t_bam |
Tumor BAM file. Required |
n_bam |
Normal BAM file. Recommended |
build |
Default hg19. Mutually exclusive with 'loci'. Currently supported 'hg19' and 'hg38' and includes ca. 900K SNPs from Affymetrix Genome-Wide Human SNP 6.0 Array. SNP file has no 'chr' prefix. |
prefix |
Prefix to add or remove from contig names in loci file. For example, in case BAM files have ‘chr' prefix, set prefix = ’chr' |
add |
If prefix is used, default is to add prefix to contig names in loci file. If false prefix will be removed from contig names. |
mapq |
Minimum mapping quality. Default 10 |
sam_flag |
SAM FLAG to filter reads. Default 1024 |
loci |
A tab separated file with chr and position. If not available use 'build' argument. |
fa |
Indexed fasta file. If provided, extracts and adds reference base to the output tsv. |
op |
Output file basename. Default parses from BAM file |
zerobased |
are coordinates zero-based. Default FALSE. Use only if 'loci' is used. |
nthreads |
Number of threads to use. Default 4. Each chromosome will be launched on a separate thread. Works only on Unix and macOS. |
verbose |
Default TRUE |
prepAscat
prepAscat_t
segmentLogR
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.