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

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