How to use Gramtools build based on multiple VCF files?

[cvn001]

Hello,

I want to build a genome graph based on VCF files of variant information for hundreds of samples.

Below I tested two samples using the following commands:

gramtools build -o ./gram --ref ref.fna --vcf A4303.vcf A4408.vcf --max_threads 64 --force

All processes run successfully, but there are the following warnings in the command line output:

2023-09-08 11:02:02,229 gramtools INFO Running vcf_record_clustering on [PosixPath('VCF/A4303.vcf'), PosixPath('VCF/A4408.vcf')].
WARNING:root:Using first sample name found "A4303". Found a different (or no) sample name "A4408", which will not be used

Does the above warning have any impact on the results?

[bricoletc]

Hi @cvn001, in terms of the built genome graph (i.e., if you don't care about sample names), no impact, the warning just states that variants from your two VCF files were combined together ('clustered') and the resulting combined VCF uses the first sample name found to express the combined variants.