Hi guys, I am trying to compare 3 vcf files using vcftools "vcf-compare" command. At first the command as follows:

vcf-compare  Ensembl1.vcf.gz dbSNP_combined_SNPs.vcf.gz filtered.snps.vcf.gz| grep "^VN"

The output was the 7 lines that I could use to generate a venn diagram.**

VN      1937     filtered.snps.vcf.gz (0.0%)    Ensembl1.vcf.gz (0.0%)

VN      14868   Ensembl1.vcf.gz (0.3%)

VN      15242    filtered.snps.vcf.gz (0.2%)    dbSNP_combined_SNPs.vcf.gz (0.3%)

VN      78896   dbSNP_combined_SNPs.vcf.gz (1.6%)

VN      2007516 Ensembl1.vcf.gz (40.8%)  dbSNP_combined_SNPs.vcf.gz (40.2%)

VN      2890237 filtered.snps.vcf.gz (35.6%)   Ensembl1.vcf.gz (58.8%)  dbSNP_combined_SNPs.vcf.gz (57.9%)

VN      5221242 filtered.snps.vcf.gz (64.2%)

Then, I downloaded an updated version of the Ensembl1.vcf.gz and ran the same command above but it only gave me the following 6 lines.

VN      31       dbSNP_combined_SNPs.vcf.gz (0.0%)

VN      1937    filtered.snps.vcf.gz (0.0%)    Ensembl1.vcf.gz (0.0%)

VN      14868   Ensembl1.vcf.gz (0.3%)

VN      2086381 Ensembl1.vcf.gz (41.7%)  dbSNP_combined_SNPs.vcf.gz (41.8%)

VN      2905479  filtered.snps.vcf.gz (35.7%)   Ensembl1.vcf.gz (58.0%)  dbSNP_combined_SNPs.vcf.gz (58.2%)

VN      5221242  filtered.snps.vcf.gz (64.2%)

Is there a reason why one of the lines was dropped or excluded from the output this time. Its not like I changed the command or anything. I just updated one of the input files.

Any help with this is highly appreciated. Thank you