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This article mainly shows you "what is the use of Control-Freec tools", the content is simple and easy to understand, clear organization, I hope to help you solve doubts, let Xiaobian lead you to study and learn "what is the use of Control-Freec tools" this article bar.

Control-Freec can detect both copy number variation CNV and loss of heterozygosity LOH. Official website as follows

http://boevalab.com/FREEC/

When detecting copy number variation, it supports multiple sequencing schemes such as whole genome sequencing, whole exon sequencing, target region capture sequencing, etc. For whole genome data, control samples are not required for analysis; for whole exon sequencing and target region capture sequencing, control samples must be provided.

The latest version of the software only supports Linux and Mac OS two operating systems, github provides compiled binary files, download and decompress directly.

The installation process is as follows

wget -O FREEC-11.4.tar.gz https://github.com/BoevaLab/FREEC/archive/v11.4.tar.gztar xzvf FREEC-11.4.tar.gzcd FREEC-11.4

There are three directories under FREEC-11.4: the data directory stores configuration file templates, including WGS and WES templates; the scripts directory contains some commonly used scripts; and the src directory is the source code of the software, where the freec executable files are located.

The first step in using the software is to edit the configuration file, which mainly includes the following five parts

1. general

Common configurations are as follows

[general]chrLenFile = test/hg19.fa.faiploidy = 2breakPointThreshold = .8#coefficientOfVariation = 0.01window = 50000#step=10000chrFiles = path/hg19/GCcontentProfile = GC_profile_50kb.cnp

chrLenFile A file specifying the chromosome length of a reference species. An example is

1 chr1 2472497192 chr2 2429511493 chr3 199501827

There are three columns in total, the first column is the number, the second column is the chromosome name, and the fourth column is the chromosome length. Note that the software only analyzes chromosomal regions that appear in the file.

ploidy specifies the number of chromosomes of the reference species. Usually we are analyzing CNV of human beings. Human is a diploid organism. The value of this parameter is 2.

The official recommended range for breakPointThreshold is 0.01 to 0.08, with lower values predicting more CNVs.

Freec predicts CNV by analyzing the sequencing depth of a certain region. For whole genome data, the analysis is performed according to the sliding window model. The window parameter specifies the size of the window and step specifies the step size. For whole exon data, the sequencing depth is calculated according to the exon region, so the window is set to 0.

When no control sample is provided, the chrFiles and GCcontentProfile parameters must be set.

The value of the chrFiles parameter is a directory containing fasta-formatted sequences for each chromosome.

The value of the GC contentProfile parameter is a file that records the GC content in the fixed window region on the chromosome and can be generated by gccount software. example is as follows

1 0 0.45896 11 50000 0.38424 11 100000 0.43834 1

There are four columns in total, the first is chromosome name, the second is the starting position of the window, the coordinates are calculated from 0, the third is GC content in the window, and the fourth column is the proportion of fuzzy bases in the window.

2. sample

Common configurations are as follows

[sample]mateFile = /path/sample.baminputFormat = BAMmateOrientation = RF

The mateFile parameter specifies the input file of the sample to be analyzed, which is usually in bam format, but also supports SAM, pillup and other formats;inputFormat specifies the format of the input file;mateOrientation specifies the sequencing direction. For single-end sequencing data, the corresponding value is 0; for illumina double-end sequencing reads, the corresponding value is FR. If the input bam file is a sorted bam file, you need to set the value of this parameter to 0.

3. control

Common configurations are as follows

[control]mateFile = /path/sample.baminputFormat = BAMmateOrientation = RF

Set the input file for the control sample, the same as the sample settings.

4. BAF

Common configurations are as follows

[BAF]SNPfile = hg19_snp138.vcf

SNPfile Specifies a file of known SNP loci in the format VCF.

5. target

Common configurations are as follows

[target]captureRegions = testChr19/capture.bed

The captureRegions parameter is a file in bed format, specifying the target region to capture. There are 3 columns in total. The first column is the chromosome name, and the second and third columns are the start and end positions of the region respectively.

For experimental designs without control samples, only general and sample need to be configured for actual analysis. BAF only needs to be configured when the input file format is pileup and B allele frequency and genotype need to be calculated. For more configuration options, please refer to the official documentation.

After editing the configuration file, you can run the command as follows

freec -config.txt Above is "Control-Freec tool what to use" All the content of this article, thank you for reading! I believe that everyone has a certain understanding, hope to share the content to help everyone, if you still want to learn more knowledge, welcome to pay attention to the industry information channel!

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