Central hub and likely the only script most users will ever interact directly with.

$ echo "Running MIP on Uppmax, analyzing all samples in family 10"
$ -c CMMS_Uppmax_config.yaml -f 10

Sequence QC

Raw sequence quality control: FastQC


Currently MIP supports these aligners:

  1. Mosaik (WES, WGS)
  2. BWA (WES, WGS, Rapid WGS)

BAM file manipulation

  • Sorting and indexing: PicardTools (SortSam)
  • Duplicate marking: PicardTools (MarkDuplicates & MarkDuplicatesWithMateCigar)
  • Realignment and base recalibration: GATK (Realigner & BaseRecalibration)

Coverage QC

Variant calling

  • Variant discovery and recalibration: GATK (HaploTypeCaller, GenoTypeGVCFs & VariantRecalibration)

Variant QC

  • All variants: GATK (VariantEval)
  • Exonic variants: GATK (VariantEval)

Variant Selection

Select transcripts that overlap a gene list: vcfParser

Variant annotation

Collect transcript and amino acid information and information from external databases as well as annotation of inheritance models: VEP, vcfParser, SnpEff, ANNOVAR, GENMOD

Variant evaluation

Score and rank each variant using weighted sums according to disease causing potential: GENMOD score (see genmod_score)

Collects QC data from the MPS analysis in YAML format. (see QCCollect).

covplots_exome.R / covplots_genome.R

Plots coverage across chromosomes.