VCF file read bug

[BanafshehKhaki]

Hello,

I have a VCF file with three samples, I notice that when I remove common regions between samples (remaining with a VCF file that has one sample per site), demuxlet cannot read in the VCF file and raises an ERROR :
NOTICE [2022/03/13 16:35:22] - Finished identifying 3 samples to load from VCF/BCF
NOTICE [2022/03/13 16:35:22] - Reading 10000 variants at chr5:74778597, Skipping 9999, Missing 0.

FATAL ERROR -
[E:int32_t main(int32_t, char**) Cannot read any single variant from

However if I keep the sites having multiple samples, it works quite fine.

To check my VCF file is not the issue: I put only few lines of sites sharing multiple samples in my VCF and demuxlet can run it without error but the results are all AMB.

I appreciate any insights on this, am not sure what the maximum likelihood to determine the best-matching sample would fail?

Thank you

[yangchao4]

Hello, I also encountered the same error. May I ask how you eventually resolved it?

[BanafshehKhaki]

Hello, as I recall, I ended up using VCF that has common regions between samples.