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SnpSift Variant type

Adds variant type annotations to the INFO field of a VCF file.

Usage

java -jar SnpSift.jar varType file.vcf > annotated.vcf

Output is written to STDOUT.

Annotations added

The command adds the following INFO fields:

  • Variant type flag: SNP, MNP, INS, DEL, or MIXED
  • Zygosity flag: HOM or HET (only meaningful for single-sample VCF files)
  • VARTYPE: Comma-separated list of variant types, one per allele

Example

$ java -jar SnpSift.jar varType test.vcf | grep -v "^#" | head
20  10469   .   C   G   100.0   PASS    SNP;HOM GT:AP   0|0:0.075,0.060
20  10492   .   C   T   100.0   PASS    SNP;HET GT:AP   0|1:0.180,0.345
20  10575   .   C   CG  100.0   PASS    INS;HET GT:AP   0|1:0.000,0.000
20  10611   .   CG  C   100.0   PASS    DEL;HET GT:AP   0|1:0.000,0.010
20  10618   .   GT  TA  100.0   PASS    MNP;HET GT:AP   0|1:0.020,0.030