Copy number variation analysis - facets
facets 是存储在 GitHub 上的R包。
factes 的开发基于 ASCN(allele-specific copy number) 分析，适用于全基因组测序(WGS)及全外显子测序(WES)。
facets 整合了BAM文件预处理、总信号和等位基因特异信号的分层联合处理，最终整合计入肿瘤纯度 (tumor purity)、倍性 (ploidy)、克隆异质性 (clonal heterogeneity) 的计算，并将结果可视化。
Input
Option 1: BAM & VCF input
- A bam file of the tumour sample
- A bam file of the normal sample (typically, a blood sample from the same patient)
- A VCF file of common, polymorphic SNPs.
Option 2: Pileup input
以 Option 1 的 BAM 文件为对象，运行脚本 cnv_facets.R ，得到一个以逗号分隔的文件，包含参考基因组的读数及多态SNP的等位基因。一般有以下几列：
- Chromosome Chromosome of the SNP
- Position Position of the SNP
- File1R Read depth supporting the REF allele in normal sample
- File1A Read depth supporting the ALT allele in normal sample
- File2R Read depth supporting the REF allele in tumour sample
- File2A Read depth supporting the ALT allele in tumour sample
Output
CNV profile plot
主要看这张图。
依然直接拿 Boss Jimmy 给的文件看一眼。
- The top panel displays total copy number log-ratio (logR),
- and the second panel displays allele-specific log-odds-ratio data (logOR) with chromosomes alternating in blue and gray.
- The third panel plots the corresponding integer (total, minor) copy number calls.
除此之外还有
-
VCF file compressed and indexed of copy number variants.
Tag Type Description SVTYPE String Type of structural variant SVLEN Integer Difference in length between REF and ALT alleles END Integer End position of the variant described in this record NUM_MARK Integer Number of SNPs in the segment NHET Integer Number of SNPs that are deemed heterozygous CNLR_MEDIAN Float Median log-ratio (logR) of the segment. logR is defined by the log-ratio of total read depth in the tumor versus that in the normal CNLR_MEDIAN_CLUST Float Median log-ratio (logR) of the segment cluster. logR is defined by the log-ratio of total read depth in the tumor versus that in the normal MAF_R Float Log-odds-ratio (logOR) summary for the segment. logOR is defined by the log-odds ratio of the variant allele count in the tumor versus in the normal MAF_R_CLUST Float Log-odds-ratio (logOR) summary for the segment cluster. logOR is defined by the log-odds ratio of the variant allele count in the tumor versus that in the normal SEGCLUST Integer Segment cluster to which the segment belongs CF_EM Float Cellular fraction, fraction of DNA associated with the aberrant genotype. Set to 1 for normal diploid TCN_EM Integer Total copy number. 2 for normal diploid LCN_EM Integer Lesser (minor) copy number. 1 for normal diploid CNV_ANN String Annotation features assigned to this CNV -
Histograms of depth of coverage
Histograms of the distribution of read depth (coverage) across all the position in the tumour and normal sample, before and after filtering positions.
-
Diagnostic plot
This is a diagnostic plot to check how well the copy number fits work. For a good fit, the segment summaries should be close to one of the lines.
The copy-number log ratio that corresponds to a diploid segment is reported as the dipLogR value.
-
Pileup file
File of nucleotide counts at each SNP in normal and tumour sample.
Reference
- Shen R, Seshan VE. FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Nucleic Acids Res. 2016;44(16):e131. doi:10.1093/nar/gkw520
- Detect somatic copy number variants (CNV) in tumour-normal samples using the facets package https://github.com/dariober/cnv_facets#input
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