Quickstart

  • Create a new working directory
  • Put the probes.csv file into the working directory (download probes.csv example)
  • Put the targets.csv file into the working directory (download targets.csv example)
  • Create a subdirectory called reads_in/ in the working directory and copy your zipped sample FASTQ files (ending in .fastq.gz) into it
  • Open a terminal and change into the working directory
  • Do a dry run: amplimap
  • Run amplimap: amplimap --run

Pipeline overview

  1. Clip off UMIs (if any), identify probe by matching known probe arms to the beginning of both reads, trim off probe arms, optionally trim low-quality bases (→ parsed FASTQ files)
  2. Align parsed reads (without arms) to reference genome (→ BAM files)
  3. Calculate alignment stats
  4. Germline variant calling and annotation (e.g. to call variants in resequencing data):
    1. Calculate coverage across target regions
    2. Call variants on raw reads in target regions
    3. Call variants on UMI deduplicated reads (not consensus) in target regions
    4. Annotate coverage and variant tables with sample information
  5. Per-basepair pileups (e.g. to find low-frequency somatic mutations):
    1. Calculate consensus pileup for target regions
    2. Calculate consensus pileup for known SNPs (if provided)