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statgen / demuxlet

Genetic multiplexing of barcoded single cell RNA-seq
Apache License 2.0
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VCF file read bug #91

Open BanafshehKhaki opened 2 years ago

BanafshehKhaki commented 2 years ago

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 commented 10 months ago

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

BanafshehKhaki commented 10 months ago

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