Description Usage Arguments Author(s)
Wrapper function for CrossLinkR package
1 2 3 | crossLinkR(bamFile, vcfFile, outputfolder = "./CrossLinkR_analysis",
yieldSize = 1e+05, readLen = 100, min.mapq = 10, min.baseq = 20,
nCPU = 3, blacklist = NULL)
|
bamFile |
Bamfile with paired-end reads sorted by readName. |
vcfFile |
VCF file containing phased alleles |
outputfolder |
Output directory. If non-existent it will be created. |
yieldSize |
Number of reads to be loaded as a chunk to save memory (Default: 1000000) |
readLen |
Length of the read in bp. |
min.mapq |
Minimum mapping quality of any given read. |
min.baseq |
Minimum base quality to consider SNV for crosslink. |
nCPU |
The number of CPUs to use. Should not be more than available on your machine. |
blacklist |
List of regions to be excluded from the analysis (format: chromosome start end) |
David Porubsky
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