Variant Analysis

GEMINI mendel_errors
Function: Identify non-mendelian transmission
Usage: gemini mendel_errors --columns "chrom,start,end" test.mendel.db --gt-pl-max 1
GEMINI windower
Function: Conducting analyses on genome “windows”.
Usage: gemini windower -w 50000 -s 0 -t nucl_div -o mean my.db
Varscan
Function: VarScan performs variant detection for massively parallel sequencing data, such as exome, WGS, and transcriptome data. It calls variants from a mpileup dataset and produces a VCF 4.1
Usage: java -jar VarScan.jar [COMMAND] [OPTIONS]
GEMINI actionable_mutations
Function: This tool reports actionable mutations as well as their known drug interactions (if any) from DGIdb.
Usage: gemini actionable_mutations tumor_normal.db
GEMINI load
Function: Loading a VCF file into GEMINI
Usage: gemini load -v my.vcf -p my.ped my.db
VarScan
Function: Make consensus calls (SNP/Indel/Reference) from a mpileup file based on user-defined parameters
Usage: java -jar VarScan.jar mpileup2cns [mpileup file] OPTIONS
GEMINI gene_wise
Function: The gemini query tool allows querying by variant and the inheritance tools described above enable querying by gene for fixed inheritance patterns. The gene_wise tool allows querying by gene with custom genotype filters to bridge the gap between these tools.
Usage: gemini gene_wise $db --min-filters 3 --gt-filter "gt_types.fam1_kid == HET and gt_types.fam1_mom == HOM_REF and gt_types.fam1_dad == HOM_REF" --gt-filter "gt_types.fam2_kid == HET" --gt-filter "gt_types.fam3_kid == HET" --columns "chrom,start,end,gene,impact,impact_severity" --filter "max_aaf_all < 0.005"
vg
Function: create "augmented graph" (original graph plus new newly called stuff) and project to calls in vcf format
Usage: vg call graph.vg graph.pileup > calls.vcf
vg
Function: simulate a bunch of 150bp reads from the graph and map them
Usage: vg map -r <(vg sim -n 1000 -l 150 -x x.xg ) -x x.xg -g x.gcsa -k 22 >aln.gam
vg
Function: Variation graph construction
Usage: vg construct -r small/x.fa -v small/x.vcf.gz >x.vg
GEMINI stats
Function: The stats tool computes some useful variant statistics.
Usage: gemini stats --tstv my.db
vg
Function: create pileup for every graph position and edge in the graph
Usage: vg pileup graph.vg filtered.gam -w 40 -m 10 -q 10 > graph.pileup
VarScan
Function: Reports the read counts for each base at positions in a pileup file
Usage: java -jar VarScan.jar readcounts [pileup file] OPTIONS
vg
Function: vg view provides a way to convert the graph into various formats
Usage: vg view x.vg >x.gfa
GEMINI amend
Function: The amend tool allows one to provide an updated PED file as input and it will update each sample_id in the PED file that matches a sample_id.
Usage: gemini load -v my.vcf -p samples.ped -t VEP my.db