mapping.rules¶

The mapping.rules pipeline performs alignment for paired end fastq sequence data at the sample, and outputs BAMs and related information. Those BAMs can be used for downstream analysis including variant calling, concordance analysis and other analyses.

This pipeline contains the rules for a SnakeMake workflow for mapping reads to a reference genome and performing various analyses on the mapped data.

The rules in this file include: - end: A rule that specifies the input and output files for generating a multiqc report. - mapping: A rule that maps the reads to the reference genome using BWA and generates a BAM file. - MergeBamLanes: A rule that merges BAM files from different lanes into a single BAM file. - MarkDuplicates: A rule that marks duplicate reads in the BAM file. - CoverageReport: A rule that calculates coverage statistics from the deduplicated BAM file. - genomeCov: A rule that generates a coverage file for the entire genome using the bamcov tool. - deeptoolsCov: A rule that generates coverage statistics using the plotCoverage tool from the deeptools package. - goleftCov: A rule that generates coverage statistics using the goleft tool. - samtoolsStats: A rule that generates various statistics using the samtools package. - multiqcCoverage: A rule that generates a multiqc report from the coverage statistics generated by the other rules.

Each rule specifies the input and output files, as well as any parameters and shell commands that need to be executed.

Pipeline overview¶

• You have checked the QC of the FASTQ data using the readQC pipeline
• You have trimmed the FASTQ data using the trimming pipeline if the read quality was poor based on the readQC pipeline. OR you have skipped trimming if the read quality was good and there we no remaining adapters.
• You have filled out the config_main.yaml file with the appropriate information.
• You have installed base snakemake environment using conda env create -f envs/snake_env.yaml and activated it using conda activate snake_env

Usage¶

Testing on IBU¶

This command uses a test dataset

snakemake --np -s workflow/mapping.rules --profile slurm 2>&1 | tee logs/log_map.txt

Running on IBU¶

You should run this in a screen session.

Note: if you are having issues running Snakemake or need reminders, check out the Snakemake page.

snakemake -s workflow/mapping.rules --profile slurm 2>&1 | tee logs/log_map.txt