Different pangolin lineages given variant caller

[GoncheDanesh]

Hi,

First, thank you for this great tool. I have a list of different pipelines to test, and yours is the only one that got installed and runs easily!

I ran your pipeline on my fastq files and in the results directory I got different fasta files, one for each VCF file as explained. All of them except for the lofreq resulted as a BA.2 lineage et the lofreq one was B.1.1.529.

How do I know which tool's results I should keep?

Thanks,
Best