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Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls

License: GNU General Public License v3.0

Perl 37.42% R 55.91% Shell 6.67%

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quandico's Issues

Tips: Perl modules to install on Ubuntu

I had to rerun the installation script bash install.sh many times to install the missing modules for quandico. Want to put them up here for future users:

sudo apt-get install libenv-path-perl libgetopt-long-descriptive-perl libdatetime-perl libtest-script-perl

Missing gene name in PDF and VCF

Hi,

I'm having some problems with the output of Quandico, both the pdf and VCF are missing the gene names, they simply appear as chr1.1, chrX.3, etc.

I've tested quandico on the example dataset provided on the Git page and this problem still persists. I ran the example with this command line "quandico -s map=M62_NA13019.bam -s x=2 -s y=0 -r map=M62_NA12878.bam -r x=2 -r y=0 -A CNA902Y.bed -d results -b 13019_vs_12878"

Anyone else has encountered this issue?

Regards
Burton

Can I use quandico for whole exome data?

This question is added here because I have been asked on a separate channel. It is possible from a technical point of view, but it is not recommended. The tool quandico is designed for a targeted approach, dealing with a few hundreds of primers and some roughly double-digit number of targeted genes. That is what quandico was designed for (sparse and scattered read-depth data, with lots of non-targeted genome sequence in between).

A complete exome (for example AmpliSeq) should be analyzed by other methods, specializing on larger data-sets. Whole-exome data are almost "continuous", so established segmentation algorithms, that are part of many CNV detection methods (but not implemented in quandico), should be applied to find breakpoints and assign regions of similar copy number.

qgetcounts example output

Hi,

I am running the first part of the analysis on the example bam file (downloaded from drive) and I get different results. This is the command line:

qgetcounts -i M62_NA13019.bam -a CNA902Y.bed --samtools /opt/samtools/1.3/intel/2016/bin/samtools | head

An this is what I get:

# Creating the BAM index as the file 'M62_NA13019.bam.bai' is not there...

chr1	5923229	0	N	NPHP400001	484	NPHP4
chr1	5923339	1	N	NPHP400001	1119	NPHP4
chr1	5923335	0	N	NPHP400002	548	NPHP4
chr1	5923438	1	N	NPHP400002	553	NPHP4
chr1	5923429	0	N	NPHP400003	849	NPHP4
chr1	5923547	1	N	NPHP400003	1004	NPHP4
chr1	5923905	0	N	NPHP400004	1487	NPHP4
chr1	5924025	1	N	NPHP400004	1428	NPHP4
chr1	5923969	0	N	NPHP400005	849	NPHP4
chr1	5924081	1	N	NPHP400005	861	NPHP4

However, the output file you provide is like this:

head M62_NA13019.tsv
chr1	5923229	0	A	NPHP4	1129	NPHP4
chr1	5923335	0	A	NPHP4	586	NPHP4
chr1	5923341	1	T	NPHP4	1126	NPHP4
chr1	5923429	0	A	NPHP4	939	NPHP4
chr1	5923440	1	A	NPHP4	619	NPHP4
chr1	5923549	1	A	NPHP4	1014	NPHP4
chr1	5923905	0	T	NPHP4	1500	NPHP4
chr1	5923969	0	A	NPHP4	883	NPHP4
chr1	5924027	1	G	NPHP4	1435	NPHP4
chr1	5924046	0	C	NPHP4	970	NPHP4

Should I introduce the reference base afterwards?I don't even get the same counts (It could be because of filters) but coordinates are not the same. Do you have any idea?

Thank you in advance

Tamara

Can't access sample data on Google drive

During installation, I noticed this

[ STEP  2c ] Downloading example data ... 

https://googledrive.com/host/0BzLnl09R3GITUDZ0aXFBd2pDR0k:
2016-12-02 12:13:36 ERROR 404: Not Found.
https://googledrive.com/host/0BzLnl09R3GITWU9xTndtZE5iOEE:
2016-12-02 12:13:36 ERROR 404: Not Found.

Installation failed at step 6

I downloaded the BAM files manually and put them in the same folder with quandico. Running installation bash installation.sh failed at step 6.

# Found at least one executable(s) of 'samtools'
# /usr/local/bin/samtools = Version: 1.3 (using htslib 1.3)
# /usr/bin/samtools = Version: 0.1.19-96b5f2294a
t/10-external.t ... ok   
t/90-run.t ........ 1/4 # Testing helper scripts syntax of QUANDICO v1.14, Perl 5.018002, /usr/bin/perl
t/90-run.t ........ ok   
t/boilerplate.t ... ok   
t/manifest.t ...... skipped: Author tests not required for installation
t/pod-coverage.t .. skipped: Test::Pod::Coverage 1.08 required for testing POD coverage
t/pod.t ........... skipped: Test::Pod 1.22 required for testing POD
All tests successful.

Test Summary Report
-------------------
t/boilerplate.t (Wstat: 0 Tests: 3 Failed: 0)
  TODO passed:   1-3
Files=7, Tests=11,  2 wallclock secs ( 0.05 usr  0.02 sys +  1.72 cusr  0.17 csys =  1.96 CPU)
Result: PASS
Manifying blib/man1/qgetcounts.1p
Manifying blib/man1/qcluster.1p
Manifying blib/man1/quandico.1p
Appending installation info to /usr/local/lib/perl/5.18.2/perllocal.pod
OK.


[ STEP  6  ] Testing the installation on demo data --cp names=refGene.txt ... 

Running 'quandico' on extracted test data, this should take less than one minute ...
quandico --rexe /usr/bin/R -s data=M62_NA13019.tsv -r data=M62_NA12878.tsv -s x=2 -s y=0 -r x=2 -r y=0 --cp names=refGene.txt
Loading required package: MASS
Loading required package: grid
Loading required package: ggplot2
Loading required package: gridExtra
Loading required package: naturalsort
Loading required package: scales
Error in `$<-.data.frame`(`*tmp*`, "refcopy", value = 2) : 
  replacement has 1 row, data has 0
Calls: quandico -> import_counts -> $<- -> $<-.data.frame
Execution halted

real    0m2.055s
user    0m1.919s
sys     0m0.133s

[  RESULTS  ] You should see some files named 'sample_vs_reference.[ext]' 

ls: cannot access sample_vs_*: No such file or directory


The R package and the Perl Module (both with dependencies)
should now be installed. Please check output for errors.

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