Chapter 3 Calling CNV from Alignment file using terminal

This section will guide to use CNVpytor for calling CNV using Read depth file and incorporating variant information

3.1 Learning Objectives

This chapter will cover:

• Steps to process alignment file
• Steps to process variant information.

3.2 Calling CNV from Alignment file

The following steps can be used to process read depth information from alignment file

> cnvpytor -root file.pytor -rd file.bam

If the reference genome is human than there is no need to set the reference genome and one can run the following steps.

> cnvpytor -root file.pytor -his 1000 10000 100000
> cnvpytor -root file.pytor -partition 1000 10000 100000
> cnvpytor -root file.pytor -call 1000 10000 100000

For non human reference genome, please have a look at the section for setting reference genome.

3.3 Importing and using variant information:

> cnvpytor -root file.pytor -snp file.vcf -sample sample_name
> cnvpytor -root file.pytor -pileup file.bam                   # OPTIONAL
> cnvpytor -root file.pytor -mask_snps                         # OPTIONAL 
> cnvpytor -root file.pytor -baf 10000 100000

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