Copynumber analysis for sequence based assays (shallow Whole Genome sequncing, or targeted assays) using seqDNAcopy package from seshanv@mskcc.org
N.B. these script use a forked version of seqDNAcopy which has been updated to work with both human and mouse.
IDT_Exome_v2_Normal:~/Work/Pipelines/SeqCNV
getPairedCounts [options] TUMOR=tumor.bam NORMAL=normal.bam
Compute the binned counts from a sample pair. By default normalize
for library size and GC variation.
Options:
TUMOR=File TUMOR sample BAM file. Required.
NORMAL=File NORMAL sample BAM file. Required.
GENOME=String Genome. Default value: hg19. Possible values: {hg19, mm10}
ODIR=Directory Directory to write output files. Default: "."
GCNORM=Boolean Flag controlling whether GC-normalization is done.
Default value: TRUE. Possible Values: {FALSE, TRUE}
SAMPLEID=String Sample Id. If not specified then will form an id from
"cleaned" version of tumor and normal bam filenames
USAGE: seqSegment [options] COUNTS=counts.rda
Run the CBS algorithm on binned counts from getPairedCounts.
Options:
COUNTS=File Counts file created by getPairedCounts (Rdata file). Required.
ODIR=Directory Directory to write output files. Default value: "."
BINSIZE=(Integer|enum) Size of bins in base pairs. Default value: "auto". Possible
values: {auto,INTEGER}. If set to "auto" then determine bin
size dynamically