From VCF to AVINPUT

Question

[Can Abdullah]

I have VCF files and with the help of this bash script, I am trying to convert them to avinput file type to process faster during annotation process. But strange thing is when the conversion is complete, the number of variants increases. There are more variants in the avinput file than the vcf file. Why can this be and what should I do to match the number of variants?

The code:

ANNOVAR_PATH="Desktop/THESIS_PROJECT/annovar/"
VCF_FOLDER="Desktop/THESIS_PROJECT/PIPELINE/Picard_Outputs/CAGI5/"
OUTPUT_FOLDER="Desktop/THESIS_PROJECT/PIPELINE/Avinputs/LIFTED/CAGI5/"

for vcf_file in "$VCF_FOLDER"/*.vcf; do
    base_name=$(basename "$vcf_file" .vcf)
    "$ANNOVAR_PATH"/convert2annovar.pl -format vcf4 "$vcf_file" > "$OUTPUT_FOLDER"/"$base_name".avinput
done

[Ram]

How do you count the number of variants in each file?

[Can Abdullah]

I simply open the vcf file and avinput file to see.

[Pierre Lindenbaum]

"I open the file" doesn't mean anything. Please explain.