sequana-variant-calling 1.2.0

Description:

sequanavariantcalling 1.2.0

This is the variant_calling pipeline from the Sequana projet

Overview:
Variant calling from FASTQ files

Input:
FASTQ files from Illumina Sequencing instrument

Output:
VCF and HTML files

Status:
production

Citation:
Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352



Installation
If you already have all requirements, you can install the packages using pip:
pip install sequana_variant_calling --upgrade
Otherwise, you can create a sequana_variant_calling conda environment executing:
conda env create -f environment.yml
and later activate the environment:
conda activate sequana_variant_calling
A third option is to install the pipeline with pip method (see above) and use singularity as explained afterwards.


Usage
sequana_variant_calling --help
sequana_variant_calling --input-directory DATAPATH --reference-file measles.fa
This creates a directory variant_calling. You just need to execute the pipeline:
cd variant_calling
sh variant_calling.sh
This launch a snakemake pipeline. If you are familiar with snakemake, you can
retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:
snakemake -s variant_calling.rules -c config.yaml --cores 4 --stats stats.txt
Or use sequanix interface.


Usage with singularity::
With singularity, initiate the working directory as follows:
sequana_variant_calling --use-singularity
Images are downloaded in the working directory but you can store then in a directory globally (e.g.):
sequana_variant_calling --use-singularity --singularity-prefix ~/.sequana/apptainers
and then:
cd variant_calling
sh variant_calling.sh
if you decide to use snakemake manually, do not forget to add singularity options:
snakemake -s variant_calling.rules -c config.yaml --cores 4 --stats stats.txt --use-singularity --singularity-prefix ~/.sequana/apptainers --singularity-args "-B /home:/home"


Requirements
This pipelines requires the following executable(s):

bwa
freebayes
picard (picard-tools)
sambamba
minimap2
samtools
snpEff you will need 5.0 or 5.1d (note the d); 5.1 does not work.




Details
Snakemake variant calling pipeline is based on
tutorial
written by Erik Garrison. Input reads (paired or single) are mapped using
bwa and sorted with
sambamba-sort.
PCR duplicates are marked with
sambamba-markdup.
Freebayes is used to detect SNPs and short
INDELs. The INDEL realignment and base quality recalibration are not necessary
with Freebayes. For more information, please refer to a post by Brad Chapman on
minimal BAM preprocessing methods.
The pipeline provides an analysis of the mapping coverage using
sequana coverage.
It detects and characterises automatically low and high genome coverage regions.
Detected variants are annotated with SnpEff if a
GenBank file is provided. The pipeline does the database building automatically.
Although most of the species should be handled automatically, some special cases
such as particular codon table will required edition of the snpeff configuration file.
Finally, joint calling is also available and can be switch on if desired.


Changelog


Version
Description



1.2.0

-Xmx8g option previously added is not robust. Does not work with
snpEff 5.1 for instance.
add minimap aligner
add –nanopore and –pacbio to automatically set minimap2 as the
aligner and the minimap options (map-pb or map-ont)
add minimap2 container.
add missing resources in snpeff section



1.1.2

add -Xmx8g option in snpeff rule at the build stage.
add resources (8G) in the snpeff rule at run stage
fix missing output_directory in sequana_coverage rule
fix joint calling (regression) input function and inputs



1.1.1

Fix regression in coverage rule



1.1.0

add specific apptainer for freebayes (v1.2.0)
Update API to use click



1.0.2

Fixed failure in multiqc if coverage and snpeff are off



1.0.1

automatically fill the bwa index algorithm and fix bwa_index rule to
use the options in the config file (not the harcoded one)



1.0.0

use last warppers and graphviz apptainer



0.12.0

set all apptainers containers and add vcf to bcf conversions
Update rule sambamba to use latest wrappers



0.11.0

Add singularity containers



0.10.0

fully integrated sequana wrappers and simplification of HTML reports



0.9.10

Uses new sequana_pipetools and wrappers



0.9.5

fix typo in the onsuccess and update sequana requirements to use
most up-to-date snakemake rules



0.9.4

fix typo related to the reference-file option new name not changed
everyhere in the pipeline.



0.9.3

use new framework (faster –help, –from-project option)
rename –reference into –reference-file and –annotation to
–annotation-file
add custom summary page
add multiqc config file



0.9.2

snpeff output files are renamed sample.snpeff (instead of
samplesnpeff)
add multiqc to show sequana_coverage and snpeff summary sections
cleanup onsuccess section
more options sanity checks and options (e.g.,
genbank_file renamed into annotation_file in the config
use –legacy in freebayes options
fix coverage section to use new sequana api
add the -do-coverage, –do-joint-calling options as well as
–circular and –frebayes–ploidy



0.9.1

Fix input-readtag, which was not populated



0.9.0
First release





Contribute & Code of Conduct
To contribute to this project, please take a look at the
Contributing Guidelines first. Please note that this project is released with a
Code of Conduct. By contributing to this project, you agree to abide by its terms.