bcftools stats does not return any information on the complements

[laura-an]

Hello,

I am encountering an issue when using bcftools stats to compare two VCF files.
I have two files. 1KG_17_test.vcf.gz is a vcf from 1000 Genomes Project with only 626 samples. It follows its typical structure:

Imputed.vcf.gz is the result of removing some variants from that same file and imputing them with Impute5. It has the following structure:

I am using the following command to compare and generate stats for both files and the intersection:
bcftools stats --verbose 1KG_17_test.vcf.gz imputed.vcf.gz > statistics.txt

The problem I have is that the analysis returns results for the intersection but does not give any information on both vcf separately. These are screenshots of the file statistics.txt

I run plot-vcfstats statistics.txt -p ./plots and this is a screenshot of the file summary.pdf

I tried removing the DS on the imputed file, but results are the same. Also, I tried doing bcftools stats for both files alone and there is no problem there. The issue is when I try to compare them.

Thank you in advance.

Best regards,
Laura

[pd3]

The result suggest that all sites are present in both files. You can also try bcftools isec to get an independent view; running with -n =1 will list sites present in only one of the files.

[laura-an]

Thank you!