Analysis of modifications in cohort of 1kGP

The base and modification calling, as well as other read processing where done using in nextflow. A minimal version of nextflow 23.04.1 is required.

Dependencies

The software dependencies below should be already available at the command line in $PATH, as well as the python script in src/python directory

• Dorado version 0.7.2
• Minimap2 version 2.24-r1122
• Samtools version 1.17
• Bedtools version 2.30.0
• Modkit version 0.2.2

Calling and processing of reads

The nextflow pipeline should be executed in the next order and you should provide your yaml file containing your own parameters. The template of the config parameters can be found inside every nextflow pipeline directory in the file nextflow.config.

# Base and modification calling
nextflow run src/nextflow/basecall/main.nf \
-params-file your_custom_params.yaml

# Filter reads 
nextflow run src/nextflow/filter_reads/main.nf \
-params-file your_custom_params.yaml

# Map reads
nextflow run src/nextflow/map_reads/main.nf \
-params-file your_custom_params.yaml

# Pileup reads per haplotype
nextflow run src/nextflow/pileup_hap_mods/main.nf \
-params-file your_custom_params.yaml