Copy number variation analysis - facets

facets 是存儲在 GitHub 上的R包。

factes 的開發(fā)基于 ASCN(allele-specific copy number) 分析，適用于全基因組測序(WGS)及全外顯子測序(WES)。

facets 整合了BAM文件預(yù)處理、總信號和等位基因特異信號的分層聯(lián)合處理，最終整合計(jì)入腫瘤純度 (tumor purity)、倍性 (ploidy)、克隆異質(zhì)性 (clonal heterogeneity) 的計(jì)算，并將結(jié)果可視化。

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 文件為對象，運(yùn)行腳本 cnv_facets.R ，得到一個(gè)以逗號分隔的文件，包含參考基因組的讀數(shù)及多態(tài)SNP的等位基因。一般有以下幾列：

• 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

主要看這張圖。

依然直接拿 Boss Jimmy 給的文件看一眼。

• 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.

除此之外還有

1. 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

2. 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.

3. 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.

   https://www.biostars.org/p/250557/

4. 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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