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
- 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)
- Align parsed reads (without arms) to reference genome (→ BAM files)
- Calculate alignment stats
- Germline variant calling and annotation (e.g. to call variants in resequencing data):
- Calculate coverage across target regions
- Call variants on raw reads in target regions
- Call variants on UMI deduplicated reads (not consensus) in target
regions
- Annotate coverage and variant tables with sample information
- Per-basepair pileups (e.g. to find low-frequency somatic mutations):
- Calculate consensus pileup for target regions
- Calculate consensus pileup for known SNPs (if provided)