Installed

GRIDSS
Manta
strelka
Control-FREEC
FusorSV/SVE

GRIDSS

Property	value
prog_name	GRIDSS
paper	https://genome.cshlp.org/content/27/12/2050.full
citations_num	20 (from 2017)
obtained_from	https://github.com/PapenfussLab/gridss/releases
installed_version	2.6.3
installed_version_date	2017.10.21
newest_version	2.11
newest_version_date	2021.03.17
last_ver_check	2021.03.18
activity_main	active
activity_dev	active
issues_github	active
lang_1	java
lang_2	R
example	/opt/soft/gridss_2.5.2/example/
requirements_1	java 1.8
requirements_2	R > 3.5
install_1	foo-server
install_1_path	/opt/soft/gridss_2.6.3
install_1_admin	darked
install_1_date	2019.10.05
install_2	bar-server
install_2_path	/opt/soft/gridss_2.6.2
install_2_admin	darked
install_2_date	2019.10.05
java_ver	/opt/soft/jdk_1.8.0_212/bin/java

recommendation(s) for running it

The ENCODE DAC blacklist hg19

cd /mnt/vdb1/soft/grids_2.5.2/blacklists

wget https://www.encodeproject.org/files/ENCFF001TDO/@@download/ENCFF001TDO.bed.gz
mv ENCFF001TDO.bed.gz hg19_ENCFF001TDO.bed.gz
gunzip ENCFF001TDO.bed.gz

# BED has 411 regions

The ENCODE DAC blacklist hg38

cd /mnt/vdb1/soft/grids_2.4.0/blacklists

https://www.encodeproject.org/files/ENCFF419RSJ/@@download/ENCFF419RSJ.bed.gz

gunzip ENCFF419RSJ.bed.gz

# BED has 38 regions

installation version 2.4.0

# in a some tmp dir
wget https://github.com/PapenfussLab/gridss/archive/v2.4.0.tar.gz 
tar xfv v2.4.0.tar.gz 
cd gridss-2.4.0/


## move stuff not included in the bare jar file:
mkdir /opt/soft/grids_2.4.0/
mv -i scripts/ /opt/soft/grids_2.4.0/
mv -i example/ /opt/soft/grids_2.4.0/
mv -i docker/ /opt/soft/grids_2.4.0/
mv -i COPYING  /opt/soft/grids_2.4.0/
mv -i LICENSE.txt /opt/soft/grids_2.4.0/
mv Readme.md /opt/soft/grids_2.4.0/

# get the jar and scripts:

cd /opt/soft/grids_2.4.0/

wget https://github.com/PapenfussLab/gridss/releases/download/v2.4.0/gridss-2.4.0-gridss-jar-with-dependencies.jar 
ln -s gridss-2.4.0-gridss-jar-with-dependencies.jar gridss.jar

wget https://github.com/PapenfussLab/gridss/releases/download/v2.4.0/gridss_lite.sh
wget https://github.com/PapenfussLab/gridss/releases/download/v2.4.0/gridss.sh 

chmod uga+x scripts/*sh
chmod uga+x *sh

testing

# running:
/opt/soft/gridss_current/example/gridss.sh

old bwa BAM preprocessing

# bam2sam
samtools view -h -o R167101_S15.sam R167101_S15.bam
# set MAPQ to 0 for unmapped reads
java -jar /opt/picardtools/dist/picard.jar CleanSam I=R167101_S15.sam O=R167101_S15_cleaned.sam
# sam2bam
samtools view -bS R167101_S15_cleaned.sam > R167101_S15_cleaned.bam

STATUS 20190520

# remapped to hg19canonical using bwa mem

BAM/BAI files:
/DATA/darked89/proj/remap_20190221/grids_threaded

** important **
use run_gridss_2.2.3_threaded.sh

# it runs with 16 threads as recommended with the newest gridss version

gridss variant annotation

R packages needed

install.packages("devtools")
library(devtools)
install_github("PapenfussLab/StructuralVariantAnnotation", ref="pre_bioconductor")

modified R script

simple-event-annotation_20190520a.R
#2 be put into GitLab after success

Manta

Property	value
prog_name	Manta
publication	https://academic.oup.com/bioinformatics/article/32/8/1220/1743909
citations_num	186 (2019.05.17)
first_release_year	2015?
www	??
repo	https://github.com/Illumina/manta
lang_1	C++
lang_2	python
obtained_from	https://github.com/Illumina/manta/releases/download/v1.6.0/manta-1.6.0.release_src.tar.bz2
installed_version	1.6.0
installed_version_date	2019.06.25
newest_version	same as above
newest_version_date	same as above
last_ver_check	2020.12.31
activity_main	active?
activity_dev	??
issues_github	active
requirements_1	python 2.7
requirements_2	??
tutorial	??
test_data	??
install_1	foo-server
install_1_dir	/opt/soft/manta_1.6.0/ (src only)

## configure did ask for doxygen. installed using apt-get

running (2 stages)

# directory with links to DoD remapped to hg19 BAMs:

cd /DATA/darked89/proj/manta_testing20190520

## in fish shell
for fn in *bam
    /opt/soft/bin/configManta.py --bam=$fn --referenceFasta=/mnt/vdb1/gen/bwa_idx/hg19canon.fa --runDir=(basename $fn .bam).MantaWorkflow
    end


for fn in ./*.MantaWorkflow/runWorkflow.py
    python2 $fn --mode=local
end

Control-FREEC

Property	value
prog_name	Control-FREEC
publication	https://academic.oup.com/bioinformatics/article/28/3/423/189142
citations_num	338 (2019.04.25)
first_release_year	2012
www	http://boevalab.com/FREEC/index.html
repo	https://github.com/BoevaLab/FREEC
lang	c++
obtained_from	https://github.com/BoevaLab/FREEC/archive/v11.5.tar.gz
installed_version	11.5
installed_version_date	2018.08.05
newest_version	11.6
newest_version_date	2020.05.29
last_ver_check	2020.12.31
activity_main	active?
activity_dev	no dev branch!
issues_github	lethargic (last in Dec 2018, 20 issues open)
tutorial	http://boevalab.com/FREEC/tutorial.html
install_1	foo-server
install_1_dir	/opt/soft/freec_11.5/

requirements

R 
samtools (for .BAM for inputs)
bedtools (if using minipileup files from .BAM)
sambamba (speedup of reading of .BAM files)

testing

gem mapper mappability data needed

Property	value
prog_name	GEM
source	https://sourceforge.net/projects/gemlibrary/files/gem-library/Binary%20pre-release%203/GEM-binaries-Linux-x86_64-core_i3-20130406-045632.tbz2
version	gem_20130406
install_1	foo-server
install_1_dir	/home/darked89/soft/gem_20130406

Example command (requires the GEM genome index, valid for a certain read length)

gem-mappability -T 16 -l 100  -I Ldonovani_gen.gem.gem -o Ldonovani_gen.map100

Leishmania donovani data:

cat ~/soft/freec_current/scripts/assess_significance.R | R --slave --args ERR206539_12.ld_gen.bam_CNVs < ERR206539_12.ld_gen.bam_ratio.txt

chromosome_lengths dla hg19canon

10	chr10	135534747
11	chr11	135006516

breakdancer

# installation

git clone --recursive https://github.com/genome/breakdancer.git 
cd breakdancer
mkdir build 
cd build
cmake .. -DCMAKE_BUILD_TYPE=release 
make 
make test
cd ../..
mv -i breakdancer /opt/soft/breakdancer_20160618git/

To check later

Tangent from Broad (copy number)

https://github.com/broadinstitute/tangent https://www.biorxiv.org/content/10.1101/566505v1.abstract

Duphold 2019

https://academic.oup.com/gigascience/article/8/4/giz040/5477467

svaba 33 citat 06.2018

https://genome.cshlp.org/content/28/4/581.full repo: https://github.com/walaj/svaba

Strelka

Property	value
prog_name	strelka
paper	??
citations_num	??
www	???
repo	https://github.com/Illumina/strelka/
obtained_from	https://github.com/Illumina/strelka/releases/download/v2.9.10/strelka-2.9.10.release_src.tar.bz2
installed_version	2.9.10
installed_version_date	2018.11.08
newest_version	same as above
newest_version_date	same as above
last_ver_check	2020.12.31
activity_main	not active?
activity_dev	none
issues_github	active
lang_1	c++
lang_2	python
example	??
requirements_1	??
install_1	foo-server
install_1_path	/opt/soft/strelka_2.9.10
install_1_admin	darked
install_1_date	2019.10.29

svtools

Tools for processing and analyzing structural variants

https://github.com/hall-lab/svtools

paragraph

Graph realignment tools for structural variants

https://github.com/Illumina/paragraph

Bamginer (simulation of scv-s)

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006080

truvari

comparison of variant detected by 2 packages

https://github.com/spiralgenetics/truvari

NAIBR 10x data

https://github.com/raphael-group/NAIBR

Kevlar Titus Brown alignment free

https://github.com/kevlar-dev/kevlar

Neusomatic

https://www.nature.com/articles/s41467-019-09027-x
https://github.com/bioinform/neusomatic

abandon

SVE

Property	value
prog_name	SVE /FusorSV
publication	https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1404-6
citation_num	1 (from 2018.03.20) check: 2019.05.08
obtained_from	https://github.com/TheJacksonLaboratory/SVE
version	0.1.0
version_date	2017.12.17
last_ver_check	2019.05.08
activity_main	stalled
activity_dev	active (multiple commits, last ones2019.04.+)
issues_github	active
install_1	foo-server
install_1_path	/opt/soft/SVE

Requirements

python 2.7
HTSeq  
numpy 
scipy 
subprocess32 
bx-python 
CrossMap 
mygene
gcc 4.8 
cmake >=3.0 
Root  https://root.cern.ch/

R 3.3 or greater. You may type "make R-install" to install R-3.3.3.

Name	SVE default	SVE foo-server	Current version	Comments	Repo
BreakDancer	1.4.5	1.4.5	1.4.5	no updates?	https://github.com/genome/breakdancer
BreakSeq			2.2	Nov 2015?	repo: https://github.com/bioinform/breakseq2
cnMOPS	1.24.0		1.30.0	R package. ver date unknown??	http://www.bioinf.jku.at/software/cnmops/cnmops.html
CNVnator		0.3.3	0.4.1	update Aug 2019	https://github.com/abyzovlab/CNVnator
DELLY		0.8.1	0.8.1	update Apr 2019	https://github.com/dellytools/delly
Hydra				no updates for 4 years	https://github.com/arq5x/Hydra
LUMPY	0.2.13	0.2.13	0.3.0	updated Apr 2019	https://github.com/arq5x/lumpy-sv

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struct_soft.md

struct_soft.md

Installed

GRIDSS

recommendation(s) for running it

installation version 2.4.0

testing

old bwa BAM preprocessing

STATUS 20190520

gridss variant annotation

R packages needed

modified R script

Manta

running (2 stages)

Control-FREEC

requirements

testing

gem mapper mappability data needed

Leishmania donovani data:

chromosome_lengths dla hg19canon

breakdancer

To check later

Tangent from Broad (copy number)

Duphold 2019

svaba 33 citat 06.2018

Strelka

svtools

paragraph

Bamginer (simulation of scv-s)

truvari

NAIBR 10x data

Kevlar Titus Brown alignment free

Neusomatic

abandon

SVE

Requirements

Files

struct_soft.md

Latest commit

History

struct_soft.md

File metadata and controls

Installed

GRIDSS

recommendation(s) for running it

installation version 2.4.0

testing

old bwa BAM preprocessing

STATUS 20190520

gridss variant annotation

R packages needed

modified R script

Manta

running (2 stages)

Control-FREEC

requirements

testing

gem mapper mappability data needed

Leishmania donovani data:

chromosome_lengths dla hg19canon

breakdancer

To check later

Tangent from Broad (copy number)

Duphold 2019

svaba 33 citat 06.2018

Strelka

svtools

paragraph

Bamginer (simulation of scv-s)

truvari

NAIBR 10x data

Kevlar Titus Brown alignment free

Neusomatic

abandon

SVE

Requirements