Atlas-CNV is a method to identify copy number variants (CNVs) using Read Depth coverage at the exon level in the next-generation sequencing (NGS) of Gene Targeted Panels. Target Exons of CNVs are detected within a batch of samples (47) from the same probe capture experiment (midpool). Individually detected exons are C-scored (Z-like scores) which allows for prioritization of high quality CNVs especially for single-exon deletions or duplications. Gene and exon bar plots are also produced for additional evaluation.
Initial release used
-
Perl v5.12.2
- use strict;
- use Getopt::Long;
- use Pod::Usage;
- use Config::General;
-
R v3.1.1.
- library(reshape2)
- library("optparse")
- library(plotrix)
./atlas_cnv.pl
Usage:
atlas_cnv.pl [options] [file ...]
Options:
--config path to the configuration file [default = config]
--panel path to the panel design file (4 tab-delimited columns)
Exon_Target Gene_Exon Call_CNV RefSeq
1:1220087-1220186 SNP_1 N rs2144440
--sample path to the CNV sample tab-delimited file containing sample_id, gender, midpool
--threshold_del log2 ratio threshold to call a deletion [uses defaults in atlas_cnv.R]
--threshold_dup log2 ratio threshold to call a duplication [uses default in atlas_cnv.R]
--help|? prints a brief help message
--man prints a man page
Options:
--config-path
The path to the file containing configuration items.
--panel The path to the panel design tab-delimited file. Exon_Target,
Gene_Exon, Call_CNV, RefSeq
--sample
The path to the tab-delimited file containing sample_id, gender,
and midpool
--threshold_del
The log2 ratio threshold to call a deletion log2(sample/median)
[uses defaults in atlas_cnv.R]
--threshold_dup
The log2 ratio threshold to call a duplication
log2(sample/median) [uses defaults in atlas_cnv.R]
--help Print a brief help message and exits.
--man Prints the manual page and exits.
panel file (exact header required):
Exon_Target Gene_Exon Call_CNV RefSeq
1:1220087-1220186 SNP_1 N rs2144440
1:3083663-3083762 SNP_2 N rs2651899
1:3611843-3611942 SNP_3 N rs3765731
1:6279321-6279420 RNF207-001_18 N rs846111
1:8487274-8487373 SNP_4 N rs301797
1:11850737-11850955 MTHFR-001_11 Y NM_005957_cds_0
1:11851264-11851383 MTHFR-001_10 Y NM_005957_cds_1
1:11852335-11852436 MTHFR-001_9 Y NM_005957_cds_2
1:11853964-11854146 MTHFR-001_8 Y NM_005957_cds_3
etc...
sample file (no header): sample sex midpool
1000011111_HFG5NBCXY-1-IDMB11 F IRC_MB-MID00209.CLEMRG_1pA
1000022222_HFG5NBCXY-1-IDMB22 M IRC_MB-MID00209.CLEMRG_1pA
1000033333_HFG5NBCXY-1-IDMB33 F IRC_MB-MID00210.CLEMRG_1pA
1000044444_HFG5NBCXY-1-IDMB44 F IRC_MB-MID00210.CLEMRG_1pA
1000055555_HFG5NBCXY-1-IDMB55 M IRC_MB-MID00209.CLEMRG_1pA
etc...