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This article will explain in detail how to analyze the structural variation of breakdancer detection. The content of the article is of high quality, so the editor will share it for you as a reference. I hope you will have a certain understanding of the relevant knowledge after reading this article.

Breakdancer is a structural mutation detection software developed specifically for double-ended sequencing data at the following github address

Https://github.com/genome/breakdancer

The analysis schematic is as follows

As can be seen from the schematic diagram, breakdancer will detect the following five types of structural variations according to the comparison of double-ended reads

Insertions

Deletions

Inversions

Inter-chromosomal translocations

Intra-chromosomal translocations

The installation process of the software is as follows

Git clone-recursive https://github.com/genome/breakdancer.gitcd breakdancermkdir buildcd buildcmake.. -DCMAKE_BUILD_TYPE=release-DCMAKE_INSTALL_PREFIX=/usr/localmake

An executable binary file, breakdancer-max, is eventually generated. The use of the software is also relatively simple, a total of two steps.

1. Generate configuration file

The input file is the bam file generated by comparing the genome, and the usage is as follows

Bam2cfg.pl tumor.bam normal.bam > config.txt

In the configuration file, each sample corresponds to a row of records, containing the following eigenvalues

Readgroup:tumorplatform:illuminamap:tumor.bamreadlen:144.84lib:YLnum:10000lower:0.00upper:519.05mean:210.24std:65.87SWnormality:-40.54exe:samtools view2. Identification of structural variation

The usage is as follows

Breakdancer_max-t-Q 10-d sv.reads config.txt > sv.out

The detection of structural variation has a large amount of calculation, so it takes a long time. The output file has a large number of columns, a total of 14 columns.

Each column has the following meaning

Chromosome 1

Position 1

Orientation 1

Chromosome 2

Position 2

Orientation 2

Type of a SV

Size of a SV

Confidence Score

Total number of supporting read pairs

Total number of supporting read pairs from each map file

Estimated allele frequency

Software version

The run parameters

Columns 1 to 6 describe the location of the breakpoint; column 7 describes the type of structural variation, DEL represents deletion, INS represents insertion, INV represents inversion, ITX represents translocation on the same chromosome, and CTX represents translocation between different chromosomes; column 8 represents the length of structural variation, which has no meaning for translocation between chromosomes The ninth column represents the score of the reliability of the structural variation, and the higher the value, the higher the reliability.

On how to analyze breakdancer detection structure variation is shared here, I hope the above content can be of some help to you, can learn more knowledge. If you think the article is good, you can share it for more people to see.

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