I ran a command:
java -Xmx4g -jar snpEff.jar Mycobacterium_tuberculosis_h37rv_gca_000277735 variants.vcf > R_variants.ann.vcf -v
to annotate variants in vcf file that was produced using command:
java -jar VarScan.v2.3.9.jar mpileup2cns mydata.mpileup --min-coverage 5 --min-var-freq 0.90 --p-value 0.005 --variants > variants.vcf
The snpEff output shows SNP=0 INS=1508 Del=51 MIXED=6. However in varscan, for the same file there were 1484 SNP and 75 Indels out of 1550 SNV.
I wonder if anyone can help me get through it.