snpsift

name: snpsift description: Run SnpSift, a toolbox for filtering and manipulating annotated VCF files. Use when the user wants to filter variants, annotate with databases (dbNSFP, dbSnp, GWAS), extract fields, or manipulate VCF files. allowed-tools: Bash, Read, Grep, Glob

SnpSift is a toolbox for filtering and manipulating annotated VCF files. Once genomic variants have been annotated, SnpSift helps filter and process them to find relevant variants.

Full documentation: https://pcingola.github.io/SnpEff/

Running

Use the wrapper script at .claude/skills/snpsift/snpsift.sh. It handles JVM memory defaults and argument passthrough. The JAR file is expected at $HOME/snpEff/SnpSift.jar.

IMPORTANT: SnpSift output is typically very large (thousands to millions of lines). ALWAYS redirect output to a file. NEVER let output print to stdout, as it will fill the context window and make the conversation unusable.

# Correct: redirect to file
.claude/skills/snpsift/snpsift.sh <command> [options] [arguments] > output.vcf 2> snpsift.log

# WRONG: never do this
.claude/skills/snpsift/snpsift.sh <command> [options] [arguments]

Commands

Command	Description	Docs
`annotate`	Add ID and INFO fields from a VCF database (e.g. dbSnp)	annotate
`annotateMem`	Annotate from a VCF database loaded into memory	annotate_mem
`caseControl`	Case vs control variant comparison with p-values	casecontrol
`concordance`	Concordance metrics between two VCF files	concordance
`dbnsfp`	Annotate using dbNSFP (SIFT, Polyphen2, etc.)	dbnsfp
`extractFields`	Extract VCF fields to tab-separated format	extractfields
`filter`	Filter using arbitrary expressions	filter
`geneSets`	Annotate using MSigDb gene sets (GO, KEGG, etc.)	genesets
`gt`	Compress genotype fields	gt
`gwasCat`	Annotate using GWAS Catalog	gwascatalog
`intersect`	Intersect intervals from multiple files	intersect
`intervals`	Filter variants by BED intervals	intervals
`intervalsIndex`	Filter variants by intervals using file indexing	intervalsindex
`join`	Join files by genomic region	join
`phastCons`	Annotate using phastCons conservation scores	phastcons
`private`	Annotate private variants (family/group)	private
`rmInfo`	Remove INFO fields from VCF	rminfo
`rmRefGen`	Remove reference genotypes	rmrefgen
`split`	Split VCF by chromosome	split
`tstv`	Calculate transition/transversion ratio	tstv
`varType`	Annotate variant type (SNP, MNP, INS, DEL, MIXED)	varianttype
`vcfCheck`	Check VCF file format correctness	vcfcheck
`vcf2tped`	Convert VCF to TPED format	vcf2ped

Additional Documentation

Topic	File
Introduction	introduction
FAQ	faq
Download & Install	download
Examples	examples
Help	help