multisample vcf and Beagle

[biouserPD]

Hi,
I'd like to input SNP array data using Beagle. I have a pre-built panel. I'm having trouble figuring out how to create the input file, given the multi-sample VCF. Should I split the VCF into individual samples and specify one VCF per row in the CSV file? Or is it enough to specify the sample names and always link to the same VCF? Thanks so much for your help.

[LouisLeNezet]

Hi,
Normally this should work by giving directly your multisample vcf as one line in the csv as follow:

sample,file,index
all_samples,my_multisample.vcf.gz,my_multisample.vcf.gz.csi

I admit that this isn't quite clear in the documentation.
We will update it.

[biouserPD]

Thank you so much for the quick response. I tried what you suggested, and it works perfectly. One thing I noticed, however, is that when using a custom genome (with the --fasta option), I had to explicitly specify these commands (--igenomes_ignore --igenomes_base ./dummy_folder), otherwise the pipeline would always look for an igenome and crash with an error. I used a docker profile
Thanks again for your help.