Ryan Welch
Ryan Welch
I think if you run with `--no-phase` it will work, but as Corbin says, the program will ignore missing genotypes, so you may want to do imputation or only include...
@corbinq - I think there's also a small bug in auto-detecting unphased VCFs, see 8d74f6070a8. I'll send a PR if that looks okay to you.
Couple things to check: * Is there anything in the FILTER column other than PASS? You could try passing `--ignore-vcf-filter` to see if that helps. * What do your genotypes...
Also does this API endpoint have the phenotype groupings? Is that what is prefixed onto the phenostrings?
Apologies, Peter - I think we can actually put this on hold for now (at least from my end.) So far the LZ API seems to be able to serve...
Seems like that error message occurs when either: 1. The header row has changed (seems unlikely?) 2. The number of markers processed in the initial analysis pass does not match...
Actually I think you found the problem right there. If TRACKPOSITIONS is ON, the initial processing step does some extra checking for bad chromosomes and/or positions: https://github.com/statgen/METAL/blob/e2253cc3901df8403a331bd725d4d9fe1edfb19f/metal/Main.cpp#L1140-L1159 The `continue`s there...
It's unfortunately hard to tell from the error message. My guess is the `Error: object 'refFlat' not found` message is not the real issue, but rather something triggered later after...
The short answer is the allele order in the output does not matter. METAL flips effect sizes towards a consensus effect allele as each study is read in. The consensus...
You could try emailing the original authors to see if they would be willing to devote time/funding to it. (I am not the maintainer or author of METAL, just a...