Software Usage Function
SnpEff Available Databases java -jar snpEff.jar databases Genome This command provides a list of configured databases, i.e. available in snpEff.config file.
FreeBayes freebayes [OPTION] ... [BAM FILE] ... FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
bcftools view bcftools view [options] <in.vcf.gz> [region1 [...]] This tool converts BCF files into VCF files using BCFtools view from the SAMtools set of utilities. -i rnaseq.bam -f reference.fa -l has been developed to explore the RNA editing potential of RNA-Seq data sets using known editing events. Such events can be downloaded from DARNED database or generated from supplementary materials of a variety of publications. Known RNA editing events have to be stored in TAB files (see above for details). -i rnaseq.bam -f reference.fa has been conceived to predict potential RNA editing events using RNA-Seq data alone and without any a priori knowledge about genome information and biological properties of RNA editing phenomenon.
GEMINI de_novo gemini de_novo --columns "chrom,start,end" test.de_novo.db You can use this tool for identifying de novo (a.k.a spontaneous) mutations that arise in offspring. -i rnaseq.bam -j dnaseq.bam -f myreference.fa -o myoutputfolder is the main script devoted to the identification of RNA editing events taking into account the combined information from RNA-Seq and DNA-Seq data in BAM format. To look at potential RNA editing candidates, RNA-Seq data alone can be used.
samtools mpileup samtools mpileup [-EBugp] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]] Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample. -i rnaseq.bam -f reference.fa -F reference.2bit -o BlatCorrection -V -T requires gfServer and gfClient programs from Blat package . Reference fasta file can be converted in .2bit format using the utility faToTwoBit.
VarScan java -jar VarScan.jar pileup2snp [pileup file] OPTIONS Call SNPs from a pileup file based on user-defined parameters
GEMINI set_somatic gemini set_somatic --min-depth 30 --min-qual 20 --min-somatic-score 18 --min-tumor-depth 10 --min-norm-depth 10 tumor_normal.db Flag somatic variants. -i unselected_positions.txt -o selected_positions.txt can filter an output REDItool table according to different criteria. -i mytable -s dbsnp137.gtf.gz -S snp -o mytable_filtered -E -p filters positions of a input table according to specific annotations indexed by tabix tool. Filtered out positions will be marked with “#” at the beginning of each line. To exclude such lines the option -E should be used. Features are the same as indicated in the third field of GTF annotation file.
vg vg align -s CTACTGACAGCAGAAGTTTGCTGTGAAGATTAAATTAGGTGATGCTTG If it is a small graph, you could align to it using a full-length partial order alignment
SnpEff Download java -jar snpEff.jar download -v WBcel215.69 This command downloads and installs a database.
GEMINI mendel_errors gemini mendel_errors --columns "chrom,start,end" test.mendel.db --gt-pl-max 1 Identify non-mendelian transmission
GEMINI windower gemini windower -w 50000 -s 0 -t nucl_div -o mean my.db Conducting analyses on genome “windows”.
Varscan java -jar VarScan.jar [COMMAND] [OPTIONS] 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
GEMINI actionable_mutations gemini actionable_mutations tumor_normal.db This tool reports actionable mutations as well as their known drug interactions (if any) from DGIdb.
GEMINI load gemini load -v my.vcf -p my.ped my.db Loading a VCF file into GEMINI