| Usage | Requirement |
|---|---|
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- AIM
- WARNINGS
- CONTENT
- INPUT
- HOW TO RUN
- OUTPUT
- VERSIONS
- LICENCE
- CITATION
- CREDITS
- ACKNOWLEDGEMENTS
- WHAT'S NEW IN
- Basic quality control of initial file structures (genotypes, pedigree information, SNP allele frequencies and SNP positions on human reference genome).
- Quality control analysis and file preparation by the Alohomora and Merlin softwares (gender check, filiation check, removal of uninformative SNPs and SNPs with Mendelian errors).
- Linkage and information analysis by the Merlin software. See the tutorial and other info here.
The script does not perform any filtering regarding call rate, standard deviation of the log R ratio (LRR) and B allele frequency (BAF) of the SNPs. Please, contact me if you need my R script to do that.
| Files and folder | Description |
|---|---|
| main.nf | File that can be executed using a linux terminal, a MacOS terminal or Windows 10 WSL2. |
| nextflow.config | Parameter settings for the main.nf file. Users have to open this file, set the desired settings and save these modifications before execution. |
| bin folder | Contains files required by the main.nf file. |
| Licence.txt | Licence of the release. |
| Required files |
|---|
| A genotype file. |
| An allelic frequency file. |
| A map file. BEWARE: no space allowed in the Header. |
| A pedigree file. |
| A pedigree file. |
See the Alohomora_Format.doc in https://gmc.mdc-berlin.de/alohomora/docs.zip.
The dataset used in the nextflow.config file, as example, is available at https://zenodo.org/records/10689924.
| File name | Description |
|---|---|
| genotype.tsv | Genotype file. Available here. |
| freq_NFE_hg19.txt | Allelic frequency file. Available here. |
| map_hg19.txt | Map file. Available here. |
| pedigree.txt | Pedigree file. Available here. |
| hg19_grch37p5_chr_size_cumul.txt | Coordinates of the hg19_grch37p5 Human Genome for plots. Available here. |
Installation of:
nextflow DSL2
Graphviz, sudo apt install graphviz for Linux ubuntu
Apptainer
- Mount a server if required:
DRIVE="Z" # change the letter to fit the correct drive
sudo mkdir /mnt/share
sudo mount -t drvfs $DRIVE: /mnt/share
Warning: if no mounting, it is possible that nextflow does nothing, or displays a message like:
Launching `main.nf` [loving_morse] - revision: d5aabe528b /mnt/share/Users
- Run the following command from where the main.nf and nextflow.config files are (example: \wsl$\Ubuntu-20.04\home\gael):
nextflow run main.nf -c nextflow.config
with -c to specify the name of the config file used.
Run the following command from where you want the results:
nextflow run gael-millot/genetic_linkage # github, or nextflow run http://github.com/gael-millot/genetic_linkage
nextflow run -hub pasteur gmillot/genetic_linkage -r v1.0.0 # gitlab
Copy-paste this after having modified the EXEC_PATH variable:
EXEC_PATH="/pasteur/helix/projects/BioIT/gmillot/genetic_linkage" # where the bin folder of the main.nf script is located
export CONF_BEFORE=/opt/gensoft/exe # on maestro
export JAVA_CONF=java/13.0.2
export JAVA_CONF_AFTER=bin/java # on maestro
export APP_CONF=apptainer/1.3.5
export APP_CONF_AFTER=bin/apptainer # on maestro
export GIT_CONF=git/2.39.1
export GIT_CONF_AFTER=bin/git # on maestro
export GRAPHVIZ_CONF=graphviz/2.42.3
export GRAPHVIZ_CONF_AFTER=bin/graphviz # on maestro
MODULES="${CONF_BEFORE}/${JAVA_CONF}/${JAVA_CONF_AFTER},${CONF_BEFORE}/${APP_CONF}/${APP_CONF_AFTER},${CONF_BEFORE}/${GIT_CONF}/${GIT_CONF_AFTER}/${GRAPHVIZ_CONF}/${GRAPHVIZ_CONF_AFTER}"
cd ${EXEC_PATH}
chmod 755 ${EXEC_PATH}/bin/*.*
module load ${JAVA_CONF} ${APP_CONF} ${GIT_CONF} ${GRAPHVIZ_CONF}
Modify the second line of the code below, and run from where the main.nf and nextflow.config files are (which has been set thanks to the EXEC_PATH variable above):
HOME_INI=$HOME
HOME="${HELIXHOME}/genetic_linkage/" # $HOME changed to allow the creation of .nextflow into /$HELIXHOME/genetic_linkage/, for instance. See NFX_HOME in the nextflow software script
nextflow run main.nf -c nextflow.config
HOME=$HOME_INI
Modify the first and third lines of the code below, and run (results will be where the EXEC_PATH variable has been set above):
VERSION="v1.0"
HOME_INI=$HOME
HOME="${HELIXHOME}/genetic_linkage/" # $HOME changed to allow the creation of .nextflow into /$HELIXHOME/genetic_linkage/, for instance. See NFX_HOME in the nextflow software script
nextflow run gael-millot/genetic_linkage -r $VERSION -c $HOME/nextflow.config #github, or nextflow run http://github.com/gael-millot/genetic_linkage -r $VERSION -c $HOME/nextflow.config
nextflow run -hub pasteur gmillot/genetic_linkage -r $VERSION -c $HOME/nextflow.config # gitlab
HOME=$HOME_INI
Unknown error accessing project `gmillot/genetic_linkage` -- Repository may be corrupted: /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot/genetic_linkage
Purge using:
rm -rf /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot*
WARN: Cannot read project manifest -- Cause: Remote resource not found: https://gitlab.pasteur.fr/api/v4/projects/gmillot%2Fgenetic_linkage
Contact Gael Millot (distant repository is not public).
permission denied
Use chmod to change the user rights. Example linked to files in the bin folder:
chmod 755 bin/*.*
An example of results is present at this address: https://zenodo.org/records/10689924/files/linkage_analysis_1708550143.zip
Description:
| Result folder | Description |
|---|---|
| reports | Folder containing the classical reports of nextflow including the nextflow.config file used. |
| merlin_reports | Folder containing all the reports of the different processes. |
| Group<GR NB>c<CHR NB>_merlin | Folder containing the information provided by Merlin for each group of patients and for each chromosome. |
| complete_lodscore.tsv | Whole Genome Lodscore. |
| cutoff<CUTOFF NB>complete_lodscore.tsv | Optional file containing the lines of the complete_lodscore.tsv file above a Lodscore threshold defined in the nextflow.config file. |
| lodscore_whole_genome.pdf | Plot of the Lodscores (both whole genome and per chromosome). Model used is indicated in the title, as well as some user settings (chr nb and lodscore cut-offs, separated by pipes). |
| lodscore_settings.pdf | Plot of the cutoff*complete_lodscore.tsv files. |
| complete_information.tsv | Information of each SNP for each group of patients. |
| infor_whole_genome.pdf | Plot of the complete_information.tsv files. |
| pedstats.markerinfo_c<CHR NB> | Marker genotype statistics (one file per chromosome). |
| pedstats_c<CHR NB>.pdf | Summary of family structure (one file per chromosome). |
| raw_snp.freq.absent.in.map.txt | raw snp in the freq file but absent in the map file. |
| raw_snp.genotype.absent.in.freq.txt | raw snp in the genotype file but absent in the freq file. |
| raw_snp.genotype.absent.in.map.txt | raw snp in the genotype file but absent in the map file. |
| raw_snp.map.absent.in.freq.txt | raw snp in the map file but absent in the freq file. |
| raw_snp.not.geno.atall.in.genotype | raw snp not genotyped in any of the indiv in the genotype file. |
| lod_data.RData | R file of the data used to generate the lodscore_whole_genome.pdf file. |
| info_data.RData | R file of the data used to generate the infor_whole_genome.pdf file. |
The different releases are tagged here.
This package of scripts can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. Distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchandability or fitness for a particular purpose. See the GNU General Public License for more details at https://www.gnu.org/licenses or in the Licence.txt attached file.
Not yet published.
Alexandre Mathieu, GHFC team, Institut Pasteur, Paris
Eric Deveaud, HPC Core Facility, Institut Pasteur, Paris
Gael A. Millot, Hub, Institut Pasteur, Paris, France
The developers & maintainers of the mentioned softwares and packages, including:
Special acknowledgement to:
- Goncalo Abecasis et al. for the release of Merlin and Pedstats.
- Franz Rüschendorf et al. for the release of Alohomora.
- In the nextflow.config file, upgrade singularity -> apptainer.
- Transfert into github
- Zenodo url added in nextflow.config
Haplotype added.
- Model option --npl --exp added
- New simple dataset
Bug fixed in clean_lod_gael.R
- Code improved so that splitting is checked for all parents present in split pedigrees at the first step of nextflow
- README improved: now dataset and results are in zenodo
code debugged
code much improved so that controls are reinforced. Non parametric analysis is back again
code improved so that chr can be missing
code improved so that any error in R subprocess should stop nextflow execution
code improved and debugged (error not anymore piped into tee notably)
Bug solved in the R_main_functions_gael_20180123.R file
Empty channel solved
pdf debugged and .Rdata returned, for making nice graphs thenafter
Small improve of main.nf file + README file
Pipeline ok. The checking process output has to be debugged (a few error messages) but not critical for the analysis
Pipeline ok but lack the information assembly and the checking part has to be debugged