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.
bash
# 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 |