This is the manual for SeqCNV.

Download SeqCNV tool

Please download the file: SeqCNV.tar.gz

Install

To install, you should run:

tar -zxvf SeqCNV.tar.gz
cd SeqCNV
make

No need to do “make install”.

Run SeqCNV

SeqCNV running is simple and quick. Only one step to run SeqCNV.

To start, you can run perl run_CNV.pl -h to see usage and options.

Usage: perl
    -h Prints this message
    -p toolpath: [Required] The path to seqcnv tools (Required tools: separate_chrom.pl, run_seqcnv_allchr.pl, report_from_tsv.pl)
    -c control: [Required] A .bam file containing the control sample.
    -t case: [Required] A .bam file containg the case sample.
    -o out_dir: [Required] The directory for all output (should be seperate for each case/control pair).
    -r target: [Required] A .bed file contaning the capture target information.

An example

Suppose I have installed SeqCNV.

Path to my case bam file is /home/case.bam.
Path to my control bam file is /home/control.bam.
Path to my target file is /home/target.bed
My SeqCNV program folder is /home/SeqCNV
I set the output path to /home/output

Then my running command is

perl /home/SeqCNV/run_CNV.pl -c /home/control.bam -t /home/case.bam -o /home/output -r /home/target.bed -p /home/SeqCNV

Then I can enjoy my coffee to wait for the results.

Result

Result tree for SeqCNV is:

output  
   |---tumor
   |---control
   |---blk
   |---tsv
   |---report

The folder ‘tumor’ contains candidate break points for each chromosome in case.
The folder ‘control’ contains candidate break points for each chromosome in control.
Files in folder ‘blk’ are blocks converted from candidate break points for case and control. All of them are in binary format. You can not see any effective information if you open them using text editor.
The folder ‘tsv’ contains temporaty output for results.
The file ‘CNV_report.txt’ in ‘report’ is the final result for SeqCNV.

Format for CNV_report.txt

Records in CNV_report.txt follows the format below:

#chr start_pos end_pos length(kb) c_on t_on r_on
chr1    152553771    152591451    37.681    1229    2272    0.524
chr1    196716471    196826740    110.270    11142    5874    1.836
chr1    207697490    207700191    2.702    1087    481    2.186
chr1    222375628    222380569    4.942    0    163    0.003
chr1    248636545    248636641    0.097    7    332    0.022
.
.
.

chr: The chromosome name for this CNV event.
start_pos: Start position for this CNV event.
end_pos: End position for this CNV event.
length(kb): Length for this CNV event.
c_on: Total number of reads in control for this CNV event.
t_on: Total number of reads in case for this CNV event.
r_on: The value of maximum penalty log-likelihood for thie CNV event.

Note if r_on value is below 0.6, type for the CNV event is Copy LOSS. If r_on value is above 1.4, type for the CNV event is Copy GAIN.