SnakeMake-Pairtools-Phased

Workflow to run analyze Hi-C data in allelic mode

Requirements

• Snakemake > 8.X

All tools are integrated in a conda environment defined in env.yaml, so run with --use-conda flag.

Inputs

• Fastq paired-ends files as _1.fastq.gz and _2.fastq.gz
• Genome bgzip2 compressed Fasta with index (samtools faidx genome.fa.gz)
• VCF with parental SNPs with each parent as a Sample, file compressed with bgzip2 and indexed with tabix

Outputs

• 01_preprocessing: Fastp reports and trimmed fastq
• 02_diplod_genome: Diplod genome fasta and BWA indexes
• 03_mapping: BAM files
• 04_pairing: pairtools parsing and deduplication
• 05_filter: pairtools phasing
• 06_stats: pairtools stats
• 07_multiqc: multiQC reports

Execution

0. Clone this repository and enter it
1. Create a custom config.yml file from the template config.yml.template
2. Activate your SnakeMake environment
3. Execute the pipeline as: snakemake -c 10 --configfile /path/to/config.yml -d output_dir --use-conda

The pipeline is mostly linear, but can be used with Slurm or similar with a proper --profile

Workflow

(C) Juan Caballero 2024