| GEMINI gene_wise |
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" |
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. |
| vg |
vg map -r <(vg sim -n 1000 -l 150 -x x.xg ) -x x.xg -g x.gcsa -k 22 >aln.gam |
simulate a bunch of 150bp reads from the graph and map them |
| vg |
vg call graph.vg graph.pileup > calls.vcf |
create "augmented graph" (original graph plus new newly called stuff) and project to calls in vcf format |
| vg |
vg construct -r small/x.fa -v small/x.vcf.gz >x.vg |
Variation graph construction |
| VarScan |
java -jar VarScan.jar readcounts [pileup file] OPTIONS |
Reports the read counts for each base at positions in a pileup file |
| GEMINI amend |
gemini load -v my.vcf -p samples.ped -t VEP my.db |
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. |
| GEMINI stats |
gemini stats --tstv my.db |
The stats tool computes some useful variant statistics. |
| GEMINI roh |
gemini roh --min-snps 50 --min-gt-depth 20 --min-size 1000000 -s S138 roh_run.db |
The ‘roh’ tool in GEMINI returns runs of homozygosity identified in whole genome data. |
| GEMINI lof_sieve |
gemini lof_sieve chr22.low.exome.snpeff.100samples.vcf.db |
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. |
| VarScan |
java -jar VarScan.jar mpileup2cns [mpileup file] OPTIONS |
Make consensus calls (SNP/Indel/Reference) from a mpileup file based on user-defined parameters |
| vg |
vg view x.vg >x.gfa |
vg view provides a way to convert the graph into various formats |
| vg |
vg pileup graph.vg filtered.gam -w 40 -m 10 -q 10 > graph.pileup |
create pileup for every graph position and edge in the graph |
| GEMINI db_info |
gemini db_info test.db |
List the gemini database tables and columns. |
| VarScan |
java -jar VarScan.jar mpileup2indel [mpileup file] OPTIONS |
Call indels from a mpileup file based on user-defined parameters |
| vg |
vg filter graph.vg alignment.gam -r 0.90 -afu -s 2 -o 0 --defray_ends 999 > filtered.gam |
filter secondary and ambiguous read mappings out of the gam |
| samtools phase |
samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] <in.bam> |
Call and phase heterozygous SNPs. |
| VarScan |
java -jar VarScan.jar pileup2cns [pileup file] OPTIONS |
Make consensus calls (SNP/Indel/Reference) from a pileup file based on user-defined parameters |
| VarScan |
java -jar VarScan.jar pileup2indel [pileup file] OPTIONS |
Call indels from a pileup file based on user-defined parameters |
| VarScan |
java -jar VarScan.jar mpileup2snp [mpileup file] OPTIONS |
Call SNPs from an mpileup file based on user-defined parameters |
| vg |
vg surject -p x -b -d x.vg.index aln.gam >aln.bam |
surject the alignments back into the reference space of sequence "x", yielding a BAM file |