This is a repo that contains installers and snakemake scripts to execute the pipelines described by Kofler et al. in popoolation 1 and 2:
-
Mapping with
bwa-mem2
-
BAM wrangling and SNP calling with
samtools
andpicard
-
Population measures with
popoolation
. Computation of expected heterozygosity h_p with a python script. -
Pairwise comparisons between populations with
popoolation2
-
Clone and install the software
git clone https://github.com/jlanga/smsk_popoolation.git smsk_popoolation cd smsk_popoolation snakemake --use-conda --create-envs-only
-
Run the test dataset:
snakemake --use-conda -c 8
-
Modify the following files:
-
config/features.yaml
: the path to the genome reference, and the names of every chromosome to be processed. -
config/samples.tsv
: paths and library information of each of the samples. -
config/params.yml
: execution parameters of different tools.
-
-
Execute the pipeline:
snakemake --use-conda -j