We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Overall, the Glow liftOver function seems to work as expected, but there is an issue when the REF/ALT alleles are swapped. Below is an example:
VCF entry: 22 16849933 . C T . . .
22 16849933 . C T . . .
Output from running Picard LiftoverVcf (see details below): 22 16369271 . T C . PASS OriginalContig=22;OriginalStart=16849933;SwappedAlleles
22 16369271 . T C . PASS OriginalContig=22;OriginalStart=16849933;SwappedAlleles
Output after running the Glow liftOver:
val df_liftOver = Glow.transform("lift_over_variants", df_b37, Map("reference_file" -> referencePath, "chain_file" -> chain)).drop("genotypes")
It appears that the Glow liftOver fails due to a “MismatchedRefAllele”.
However, the desired behavior would be as follows:
22:16369271
The text was updated successfully, but these errors were encountered:
Successfully merging a pull request may close this issue.
Overall, the Glow liftOver function seems to work as expected, but there is an issue when the REF/ALT alleles are swapped. Below is an example:
VCF entry:
22 16849933 . C T . . .Output from running Picard LiftoverVcf (see details below):
22 16369271 . T C . PASS OriginalContig=22;OriginalStart=16849933;SwappedAllelesOutput after running the Glow liftOver:
val df_liftOver = Glow.transform("lift_over_variants", df_b37, Map("reference_file" -> referencePath, "chain_file" -> chain)).drop("genotypes")It appears that the Glow liftOver fails due to a “MismatchedRefAllele”.
However, the desired behavior would be as follows:
22:16369271)The text was updated successfully, but these errors were encountered: