Release 0.2.0

This release removes all MutMap related analyses since it caused several bugs.
Instead, the pipeline now mainly outputs a GATK table of variants compatible with QTLseqR. This facilitates downstream filtering and QTL calls.

Release 0.1.0

This is the first functional release of the snakemake_bsaseq pipeline.

This pipeline takes sequencing files from a BSA-seq experiment (reference and at least one mutant) and produces:

• A multiQC report on the trimmed sequencing files.
• A combined single Variant Calling Format (VCF) file for all samples (including the reference sample).
• An annotated VCF file based using snpEff.
• A tabulated variant table to be used with QTLseqR.