SnpSift Variant Type - SnpEff & SnpSift
Author: Pablo Cingolani
Description: SnpEff and SnpSift

Skip to content

# SnpSift Variant type

Adds an INFO field denoting variant type.

It adds "SNP/MNP/INS/DEL/MIXED" in the INFO field. It also adds "HOM/HET", but this last one works if there is only one sample (otherwise it doesn't make any sense).

    $ 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    DEL;HET GT:AP   0|1:0.000,0.000
    20  10611   .   CG  C   100.0   PASS    INS;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