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