Variant calling in haploid genomes: a published workflow on usegalaxy.eu

Release 0.3 of a workflow from the Intergalactic Workflow Commission (IWC). Drag to move around and use the zoom buttons. View In Galaxy opens it on usegalaxy.eu, where a logged-in student can import it.

The workflow as a list of steps

Inputs: paired-end Illumina reads (a paired collection), a gene annotation (GTF) and a reference genome (FASTA).

  1. Trim and filter the reads (fastp).
  2. Build a SnpEff database from the annotation and genome (SnpEff build).
  3. Map the reads to the genome (BWA-MEM).
  4. Keep reads mapped in proper pairs (Samtools view).
  5. Summarise the mapping (Samtools stats).
  6. Mark duplicate reads (Picard MarkDuplicates).
  7. Combine the quality reports (MultiQC).
  8. Realign the reads (LoFreq Viterbi).
  9. Call variants (LoFreq call).
  10. Keep only single-base substitutions (Text reformatting, with awk).
  11. Predict each variant's effect on genes (SnpEff eff).
  12. Extract fields into a table (SnpSift Extract Fields).
  13. Join the samples' tables into one (Collapse Collection).