Example Use Cases

Default Run

Combine and filter variants from multiple populations, whilst also removing reference gaps.

SVPop -F=sampleFiles.txt -R=annotation.gtf -M=DEL --filterGaps=True --gapsFile=gaps.txt --subPops=pops.txt

Analysis -> Visualisation Pipeline

Perform analysis for a selection of samples, note that annotation and sub-population statistics are required for visualisation.

# Create variant & window files for each model (-R and -P are required)
../SVPop -F=sampleFiles.txt -M=DEL -R=annotation.gff -P=subpops.txt
../SVPop -F=sampleFiles.txt -M=DUP -R=annotation.gff -P=subpops.txt
../SVPop -F=sampleFiles.txt -M=INS -R=annotation.gff -P=subpops.txt
../SVPop -F=sampleFiles.txt -M=INV -R=annotation.gff -P=subpops.txt

# Prep for visualisation
../SVPop --PREPROCESS --variantFile=Merged

# Move output files to Visualisation/Files. (Must include a tsv annotation.txt file)
Rscript easyRun.r

Variant Annotation

Annotate a variant file for one or more samples by providing the sample, an annotation file, and the variant type (DEL, DUP, INS, INV) as indicated below:

SVPop -F=sampleX.vcf -R=annotation.gtf -M=DEL

Get Summary Stats

Produce summary statistics for a variant file.

SVPop --variantFile='FilePrefix' --subPops=pops.txt

Find Feature-Relevant Variants

Isolate variants that overlap a specific feature.

SVPop --variantFile=file.csv --feature=<gene_name>