| SnpSift |
Generic SnpSift tool caller
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| SnpSiftCmdAlleleMatrix |
Convert VCf file to allele matrix
Note: Only use SNPs
Note: Only variants with two possible alleles.
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| SnpSiftCmdAnnotate |
Annotate a VCF file with ID from another VCF file (database)
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| SnpSiftCmdCaseControl |
Count number of cases and controls
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| SnpSiftCmdConcordance |
Calculate genotyping concordance between two VCF files.
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| SnpSiftCmdCovarianceMatrix |
Convert allele 'matrix' file into Covariance matrix
Note: Only variants with two possible alleles.
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| SnpSiftCmdDbNsfp |
Annotate a VCF file with dbNSFP.
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| SnpSiftCmdExtractFields |
Extract fields from VCF file to a TXT (tab separated) format
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| SnpSiftCmdFilter |
Generic SnpSift filter
Filter out data based on VCF attributes:
- Chromosome, Position, etc.
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| SnpSiftCmdFilterChrPos |
Filter using CHROM:POS only
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| SnpSiftCmdFilterGt |
Generic SnpSift genotype filter
Removes genotypes matching the filter:
e.g.
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| SnpSiftCmdGeneSets |
Annotate a VCF file using Gene sets (MSigDb) or gene ontology (GO)
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| SnpSiftCmdGt |
Add genotype information to INFO fields
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| SnpSiftCmdGwasCatalog |
Annotate a VCF file using GWAS catalog database
Loads GWAS catalog in memory, thus it makes no assumption about order.
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| SnpSiftCmdIntersect |
Intersect intervals
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| SnpSiftCmdIntervals |
Filter variants that hit intervals
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| SnpSiftCmdIntervalsIndex |
Filter variants that hit intervals
Use an indexed VCF file.
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| SnpSiftCmdJoin |
Annotate a VCF file with ID from another VCF file (database)
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| SnpSiftCmdPedShow |
Draws a pedigree using SVG according to a VCF file
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| SnpSiftCmdPhastCons |
Annotate using PhastCons score files
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| SnpSiftCmdPrivate |
Annotate if a variant is 'private'.
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| SnpSiftCmdRemoveReferenceGenotypes |
Removes reference genotypes.
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| SnpSiftCmdRmInfo |
Removes INFO fields
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| SnpSiftCmdSort |
Sort VCF file/s by chromosome & position
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| SnpSiftCmdSplit |
Split a large VCF file by chromosome or bby number of lines
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| SnpSiftCmdTsTv |
Calculate Ts/Tv rations per sample (transitions vs transversions)
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| SnpSiftCmdVarType |
Annotate a VCF file with variant type
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| SnpSiftCmdVcf2Tped |
Transform a VCF to a TPED file
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| SnpSiftCmdVcfCheck |
Check VCF files (run some simple checks)
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| SnpSiftCmdVcfOperator |
Annotate a field based on an operation (max, min, etc.) of other VCF fields
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| VcfLd |
Calculate Linkage Disequilibrium
Reference: "Principles of population genetics (4th edition)" Hartl & Clark, pages 73 to 81
Note: I try to follow the same notation as the book.
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