filter_fastqs

A Snakemake pipeline that filters paired-end FASTQ files to retain only reads mapping to specified genomic regions.

Overview

Given aligned BAM files and a BED file defining regions of interest, the pipeline:

1. Sorts and indexes the BAMs
2. Extracts reads overlapping the target regions (via samtools view -L)
3. Filters the original FASTQ files to keep only those read IDs
4. Compresses the output FASTQs with pigz

Dependencies

• Snakemake
• samtools
• pigz
• Python 3 (standard library only)

Configuration

Edit the top of filter_fastqs.smk to set your paths:

aligned_bams_folder = "/path/to/aligned_bams"   # STAR-style: <folder>/<sample>/Aligned.out.bam
fastq_folder        = "/path/to/fastqs"          # paired-end: <sample>_1.fq.gz, <sample>_2.fq.gz
bed_file            = "/path/to/regions.bed"     # regions to retain
output_folder       = "/path/to/output"          # created automatically

Samples are discovered automatically from the FASTQ filenames.

Usage

snakemake -s filter_fastqs.smk --cores <N>

Output

<output_folder>/
  sorted_bams/         # coordinate-sorted BAMs and indexes
  filtered_bams/       # SAM files containing only reads in target regions
  <sample>_1.fq.gz     # filtered paired-end FASTQs
  <sample>_2.fq.gz

Helper script

scripts/get_regions.py extracts specific gene regions from a GTF into a BED file. Edit the gtf_file, output_bed_file, and the feature filter string inside the script, then run it directly with Python to generate the BED file needed for the pipeline.