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License: GNU General Public License v3.0
Quantitative analysis of differences in copy numbers using read depth obtained from PCR-enriched samples and controls
License: GNU General Public License v3.0
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
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
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.
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
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.
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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