Structure¶
mip.pl¶
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"
$ mip.pl -c CMMS_Uppmax_config.yaml -f 10
BAM file manipulation¶
- Sorting and indexing: PicardTools (SortSam)
- Duplicate marking: PicardTools (MarkDuplicates)
- Realignment and base recalibration: GATK (Realigner & BaseRecalibration)
Coverage QC¶
- Coverage Report and QC metrics: Chanjo & BedTools
- QC metrics: PicardTools (MultipleMetrics & HSmetrics)
Variant calling¶
- Variant discovery and recalibration: GATK (HaploTypeCaller, GenoTypeGVCFs & VariantRecalibration)
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: Score_mip_variants (see score_mip_variants)
covplots_exome.R / covplots_genome.R¶
Plots coverage across chromosomes.