![]() ![]() The control (matched normal) sample is optional for whole genome sequencing data but mandatory for whole exome or targeted sequencing data.įor whole genome sequencing data analysis, the program can also use mappability data (files created by Valentina Boeva at Institut Cochin, Inserm(Paris).Ĭontrol-FREEC automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. Starting from version v8.0, we provide a possibility to detect subclonal gains and losses and evaluate the likeliest average ploidy of the sample.Īlso, the procedure for evaluation of tumor purity has been improved. Input for CNA detection: aligned single-end, paired-end or mate-pair data in SAM, BAM, SAMtools pileup.Ĭontrol-FREEC accepts. Support of Eland, BED, SOAP, arachne, psl (BLAT) and Bowtie formats has been discontinued starting from version v8.0. Files can be GZipped (b) provide BAM files together with options "makePileup" and "fastaFile" (see How to create a config file?) Input for CNA+LOH detection: There are two options: (a) provide aligned reads in SAMtools pileup format. ![]()
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