Variant Analysis

Function: Identify non-mendelian transmission

Usage: gemini mendel_errors --columns "chrom,start,end" test.mendel.db --gt-pl-max 1

Function: Conducting analyses on genome “windows”.

Usage: gemini windower -w 50000 -s 0 -t nucl_div -o mean my.db

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]

Function: This tool reports actionable mutations as well as their known drug interactions (if any) from DGIdb.

Usage: gemini actionable_mutations tumor_normal.db

Function: Loading a VCF file into GEMINI

Usage: gemini load -v my.vcf -p my.ped my.db

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

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"

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

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

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

Function: The stats tool computes some useful variant statistics.

Usage: gemini stats --tstv my.db

Function: Variation graph construction

Usage: vg construct -r small/x.fa -v small/x.vcf.gz >x.vg

Function: he lof_sieve tool reports the fractional position (e.g. 0.05 for the first 5%) of the mutation in the amino acid sequence. In addition, it also reports the predicted function of the transcript so that one can segregate candidate LoF variants that affect protein_coding transcripts from processed RNA, etc.

Usage: gemini lof_sieve chr22.low.exome.snpeff.100samples.vcf.db

Function: Reports the read counts for each base at positions in a pileup file

Usage: java -jar VarScan.jar readcounts [pileup file] OPTIONS

Function: The ‘roh’ tool in GEMINI returns runs of homozygosity identified in whole genome data.

Usage: gemini roh --min-snps 50 --min-gt-depth 20 --min-size 1000000 -s S138 roh_run.db