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An open-source toolkit for large-scale genomic analysis
Looking at the [docs for splitting multiallelic variants](https://glow.readthedocs.io/en/latest/etl/variant-splitter.html), it looks like the answer is no. This differs from the hail implementation of "split_multi_hts". Should QC filters based on GQ be...
Hi, I tried to run the glow gwas logistic regression but running into errors when writing out the results at the end: Caused by: org.apache.spark.SparkException: Job aborted due to stage...
I am trying to get GLOW WGR to run using the example step by step but with own data (~300k variants in ~350k individuals, ~ 450 binary phenotypes). After writing...
The Saddle point approximation test can produce p-values that are impossibly low for variants with low minor allele count. Set a warning for users in the docs and provide a...
The GloWGR notebooks include reading of covariates & phenotypes into pandas dataframes. They work find if the `sample_id` is a string (e.g. "ID_1"), however if the `sample_id` looks like an...
When reading large `bgen` files and writing out to delta lake in cloud object storage, Spark jobs run much faster if there are many small VMs rather than a few...
When reading multiple gVCFs that have tabix indices and the same base name. It seems that the index becomes corrupted when the second gVCF is read and slicing based on...
Hi! I'd like to learn Glow but I'm having trouble running the demo-notebook (https://glow.readthedocs.io/en/latest/getting-started.html#demo-notebook) using Databricks Community Edition. Is there perhaps a way for me to obtain data used in...
Issue can be reproduced on chrY data from 1000 genomes project (release 20130502), got it on `io.projectglow:glow-spark3_2.12:0.6.0` and earlier versions. Please see code and explanations below ``` sourcefiles = "/mnt/1000-genomes/release/chrY.vcf.gz"...
We should allow the user to configure these parameters, especially for the approximate Firth fit. cc @bboutkov since I believe this came up in your tests. `logistic_regression` definition: https://github.com/projectglow/glow/blob/master/python/glow/gwas/log_reg.py#L24-L33
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An open-source toolkit for large-scale genomic analysis