Analysis: Copy Number Alterations (CNA) calling/ Copy Number Variation (CNV) calling....

Copy number alterations (CNAs) are changes in copy number that have arisen in somatic tissue

(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017908/)

Identification of gene CNAs in an individual patient’s tumor is increasingly relevant.

FASTQ files sample sheet-----Parsing---------Variant Calling--------CNA calling

Calling CNA from amplicon sequencing data is feasible. Non-tumor (germline) DNA is needed for data normalization.

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Copy Number Variation (CNV), the structural variation in the genome occur due to repetition, due to duplication or deletion

(https://en.wikipedia.org/wiki/Copy-number_variation#/media/File:Gene-duplication.png)

The BCFtools detects copy number alterations, aneuploidy and contamination.Chromosome aneuploidy (an abnormal number of chromosomes) is one cause of IVF failure as embryos with aneuploidy mostly do not implant or miscarry during the first trimester of pregnancy.

#compile with
make USE_GPL=1 clean all
#type
bcftools polysomy
#(polysomy command takes on input VCF
#Find chromosomal aberrations
bcftools polysomy -v -o outdir/ file.vcf
#results can be found in outdir/dist.dat
#See the output file
cat outdir/dist.dat | awk '$1=="CN" && $3!=2.0'
#For clean data, the third column should be 2.0 for normal diploid state, 1.0 for a loss, 3.0 for gain, and -1 is used when the program cannot determine the state, usually because of noisy data
#The distribution can be plotted using the auto-generated matplotlib script

#to detect differences between two samples
bcftools cnv -c conrol_sample -s query_sample -o outdir/ -p 0 file.vcf
The -p 0 option tells the program to automatically call matplotlib and produce plots like the one in this example
# Annotation file with BAF values for two samples
$ zcat baf.txt.gz | head -2

# Index the annotation file and fill in the BAF values. Add a BAF definition into the VCF header
$ tabix -s1 -b2 -e2 baf.txt.gz
$ echo '##FORMAT=<ID=BAF,Number=1,Type=Float,Description="NGS estimate of BAF">' > baf.hdr
$ bcftools annotate -a baf.txt.gz -h baf.hdr -c CHROM,POS,FMT/BAF -Ob -o output.bcf input.bcf