Annovar and wannovar

Question

[vaish01kv]

Hi! I tried comparing the result of wANNOVAR and ANNOVAR using the same file. Only 464 rows matched! Can someone help me to improve my result & bring the same result as wANNOVAR? TIA!

[Kevin Blighe]

Please show all of your processing steps.

[vaish01kv]

perl convert2annovar.pl -format vcf4 SampleName.vcf > converted.input
    perl table_annovar.pl converted.input humandb/ -buildver hg38 -out converted_result -remove -protocol refGene,cytoBand,cosmic70,clinvar_20190305,1000g2015aug_all,1000g2015aug_amr,1000g2015aug_afr,1000g2015aug_eas,1000g2015aug_eur,1000g2015aug_sas -operation gx,r,f,f,f,f,f,f,f,f -nastring . -csvout"
This is the command i used for running annovar.