Non overlapping samples

[zd1]

Hi there,

Thanks for making the fastqtl tool. I have been trying to test it for some of my data.

I realised that it requires the sample count in the phenotype bed and the genotype vcf to be exactly the same, as shown here:

fastqtl/src/readGenotypes.cpp

Line 55 in 4d03819

if (n_includedS != sample_count) LOG.error("Genotype data does not overlap with phenotype data, check your files!");

and throws an error otherwise.

I was wondering if this could be made slightly more friendly, for example, using only intersecting samples for further analysis.

It is not rare having slightly different numbers of samples in the genotype file and the phenotype file.

Thanks,
Zhihao

[zd1]

Sorry just realised that this is not the official repository. Never mind.

Zhihao