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Common CNV

[TOC]

Description

Call copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments using R package ExomeDepth

Install and configure

Install

# add bioconda channel
# conda config --add channels bioconda
# create a new  enviornment
$ conda create -n call_CNV
# To activate this environment, use
$ conda activate call_CNV
# install R and packages
$ conda install r-base
$ conda install -c bioconda r-exomedepth
$ conda install -c bioconda bioconductor-genomicranges

I uesd ExomeDepth(1.1.11) in this pipeline.

Inptut file

ExomeDepth requires at least 3 samples in BAM format as input, which should be sorted and with the index.

I use the chr1 fragment of three BAM files as the sample data ( sample1.bam, sample2.bam, sample3.bam).

Output file

  • ExomeCount_*.csv: CSV file for exons count;

  • Exome_*: TSV files for CNV discovery.

Configure

There are some rows in /bin/call_CNV.R must be checked/configured:

  • task_na='test' （Row 5）: Change task to the name of your task.
  • am_path <- '../input/'(Row 6)：Change ../input/ to the real input directory.
  • out_path <- '../output/'（Row 7）：Change ../output/ to the real output directory.
  • fasta <- '~/ref_v37/human_g1k_v37.fasta（Row 8）：Change ~/ref_v37/human_g1k_v37.fasta to the real reference FASTA file.

Run pipeline

$ cd bin/
$ Rscript call_CNV.R

Main Steps

  1. Create count data from BAM files
  2. Build the most appropriate reference set
  3. CNV calling

Reference