/snakemake-pairtools-phased

Primary LanguagePython

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

  1. Clone this repository and enter it
  2. Create a custom config.yml file from the template config.yml.template
  3. Activate your SnakeMake environment
  4. 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

workflow

(C) Juan Caballero 2024