usage: facets doFacets [-h] [-c CVAL] [-s SNP_NBHD] [-n NDEPTH] [-m MIN_NHET]
[-pc PURITY_CVAL] [-ps PURITY_SNP_NBHD]
[-pn PURITY_NDEPTH] [-pm PURITY_MIN_NHET] [-d DIPLOGR]
[-g GENOME] [-f COUNTS_FILE] [-t TAG] [-D DIRECTORY]
[-r R_LIB] [-C SINGLE_CHROM] [-G GGPLOT2] [--seed SEED]
optional arguments:
-h, --help show this help message and exit
-c CVAL, --cval CVAL critical value for segmentation
-s SNP_NBHD, --snp_nbhd SNP_NBHD
window size
-n NDEPTH, --ndepth NDEPTH
threshold for depth in the normal sample
-m MIN_NHET, --min_nhet MIN_NHET
minimum number of heterozygote snps in a segment used
for bivariate t-statistic during clustering of
segments
-pc PURITY_CVAL, --purity_cval PURITY_CVAL
critical value for segmentation
-ps PURITY_SNP_NBHD, --purity_snp_nbhd PURITY_SNP_NBHD
window size
-pn PURITY_NDEPTH, --purity_ndepth PURITY_NDEPTH
threshold for depth in the normal sample
-pm PURITY_MIN_NHET, --purity_min_nhet PURITY_MIN_NHET
minimum number of heterozygote snps in a segment used
for bivariate t-statistic during clustering of
segments
-d DIPLOGR, --dipLogR DIPLOGR
diploid log ratio
-g GENOME, --genome GENOME
Genome of counts file
-f COUNTS_FILE, --counts_file COUNTS_FILE
paired Counts File
-t TAG, --TAG TAG output prefix
-D DIRECTORY, --directory DIRECTORY
output prefix
-r R_LIB, --R_lib R_LIB
Which version of FACETs to load into R
-C SINGLE_CHROM, --single_chrom SINGLE_CHROM
Perform analysis on single chromosome
-G GGPLOT2, --ggplot2 GGPLOT2
Plots using ggplot2
--seed SEED Set the seed for reproducability
usage: facets mafAnno [-h] [-m MAF] [-f FACETS_FILES] [-o OUT_MAF]
optional arguments:
-h, --help show this help message and exit
-m MAF, --maf MAF file name of maf file to be annotated.
-f FACETS_FILES, --facets_files FACETS_FILES
Mapping of "Tumor_Sample_Barcode" from maf and
"Rdata_filename" from FACETS (tab-delimited with
header)
-o OUT_MAF, --out_maf OUT_MAF
file name of CN annotated maf.
usage: facets normDepth [-h] [-f FILE]
optional arguments:
-h, --help show this help message and exit
-f FILE, --file FILE Filename of counts file to be normalized.
usage: facets geneLevel [-h] [-f FILENAMES] [-o OUTFILE]
optional arguments:
-h, --help show this help message and exit
-f FILENAMES, --filenames FILENAMES
list of filenames to be processed.
-o OUTFILE, --outfile OUTFILE
Output filename.
usage: facets mergeTN [-h] [-t TUMOR_COUNTS] [-n NORMAL_COUNTS] [-o OUTFILE]
optional arguments:
-h, --help show this help message and exit
-t TUMOR_COUNTS, --tumor_counts TUMOR_COUNTS
Tumor counts file name
-n NORMAL_COUNTS, --normal_counts NORMAL_COUNTS
Normal counts file name
-o OUTFILE, --outfile OUTFILE
output file (gzipped)