# Science **URL:** https://discuss.hail.is/c/science/11.md [Latest](https://discuss.hail.is/latest.md) · [Categories](https://discuss.hail.is/categories.md) --- ## [About the Science category](https://discuss.hail.is/t/about-the-science-category/20)
**Author:** [@hail-team](https://discuss.hail.is/u/hail-team)\ **Replies:** 0
Scientific applications of Hail. Did you use Hail to refine, accelerate, or scale your analyses? To uncover the genetic basis of disease? To model the course of human history? We'd love to hear about about it! Descri… --- ## [How to calculate hemizygous counts for sex chromosome variants](https://discuss.hail.is/t/how-to-calculate-hemizygous-counts-for-sex-chromosome-variants/4191)
**Author:** [@Mireia](https://discuss.hail.is/u/Mireia)\ **Replies:** 1\ **Last updated:** [August 21, 2025, 7:22am UTC](https://discuss.hail.is/t/how-to-calculate-hemizygous-counts-for-sex-chromosome-variants/4191 "2025-08-21T07:22:40Z")
Hello! I’m building a Hail pipeline to calculate allele frequency statistics by sex and ancestry, aiming to replicate the gnomAD-style table with: Allele Count (AC) Allele Number (AN) Number of Homozygotes (n\_h… --- ## [Can't get gnomad on jupyter notebook](https://discuss.hail.is/t/cant-get-gnomad-on-jupyter-notebook/4132)
**Author:** [@complexgenome](https://discuss.hail.is/u/complexgenome)\ **Replies:** 0\ **Last updated:** [May 19, 2025, 5:55pm UTC](https://discuss.hail.is/t/cant-get-gnomad-on-jupyter-notebook/4132 "2025-05-19T17:55:22Z")
Hi there, I use minerva notebook from sinai I am interested to follow the broad tutorial I can run the following code on my command line (no jupyter notebook) Python 3.8.8 (default, Apr 13 2021, 19:58:26) import… --- ## [Simulate matrix with 'GWAS signal'](https://discuss.hail.is/t/simulate-matrix-with-gwas-signal/4006)
**Author:** [@Juan\_Felipe\_Ortiz](https://discuss.hail.is/u/Juan_Felipe_Ortiz)\ **Replies:** 0\ **Last updated:** [December 9, 2024, 10:04am UTC](https://discuss.hail.is/t/simulate-matrix-with-gwas-signal/4006 "2024-12-09T10:04:25Z")
We are evaluating methods to run GWAS and post-GWAS analyses. It would be great to be able to simulate a multi-ancestry hail matrix that causes a GWAS analysis to produce “buildings” in a Manhattan plot. Is there a para… --- ## [Request for Feedback on Hail-Adjacent System](https://discuss.hail.is/t/request-for-feedback-on-hail-adjacent-system/3878)
**Author:** [@jonahrosenblum](https://discuss.hail.is/u/jonahrosenblum)\ **Replies:** 2\ **Last updated:** [June 17, 2024, 5:40pm UTC](https://discuss.hail.is/t/request-for-feedback-on-hail-adjacent-system/3878 "2024-06-17T17:40:18Z")
Hello, I want to preface this by saying I understand this is an irregular question and that the Hail community and its developers are busy. We appreciate you taking the time to read our request. Our group at the Univer… --- ## [Reading vcf non GT column](https://discuss.hail.is/t/reading-vcf-non-gt-column/3739)
**Author:** [@Tetyana\_Zayats](https://discuss.hail.is/u/Tetyana_Zayats)\ **Replies:** 2\ **Last updated:** [February 21, 2024, 9:47pm UTC](https://discuss.hail.is/t/reading-vcf-non-gt-column/3739 "2024-02-21T21:47:58Z")
Hi, I need to read genotypes from a column other than GT in a vcf file. Does any one know how to do it in Hail? Many thanks for you help! --- ## [Calculate PGS score from UKB data using PGS Catalog](https://discuss.hail.is/t/calculate-pgs-score-from-ukb-data-using-pgs-catalog/3631)
**Author:** [@irun](https://discuss.hail.is/u/irun)\ **Replies:** 2\ **Last updated:** [November 13, 2023, 5:17pm UTC](https://discuss.hail.is/t/calculate-pgs-score-from-ukb-data-using-pgs-catalog/3631 "2023-11-13T17:17:27Z")
Hi! I am trying to calculate polygenic risk scores (PRS/PGS) for UK Biobank data (imputed bgen files) using pre-computed scores from the PGS Catalog available online. So basically I’m just trying to code a script that … --- ## [gnomAD: How are mutation rates calculated?](https://discuss.hail.is/t/gnomad-how-are-mutation-rates-calculated/3614)
**Author:** [@agastya](https://discuss.hail.is/u/agastya)\ **Replies:** 3\ **Last updated:** [November 9, 2023, 7:06pm UTC](https://discuss.hail.is/t/gnomad-how-are-mutation-rates-calculated/3614 "2023-11-09T19:06:36Z")
Hi everyone, I apologize if this question does not fall in the purview of this forum. I was going through the gnomAD constraint calculation code (https://github.com/broadinstitute/gnomad\_lof/blob/master/constraint\_utils… --- ## [LPL fields in Dragen msVCF](https://discuss.hail.is/t/lpl-fields-in-dragen-msvcf/3538)
**Author:** [@jbakewell](https://discuss.hail.is/u/jbakewell)\ **Replies:** 0\ **Last updated:** [August 8, 2023, 4:22pm UTC](https://discuss.hail.is/t/lpl-fields-in-dragen-msvcf/3538 "2023-08-08T16:22:17Z")
Hi I’m analysing multisample VCFs generated by Dragen’s iterative genotyper in Hail. Analogous to Hail’s VDS format, the VCF contains local alelles PLs (LPL) instead of the standard global PLs output by other methods. I… --- ## [Logistic regression using firth test returns N](https://discuss.hail.is/t/logistic-regression-using-firth-test-returns-n/3466)
**Author:** [@hirbokazi](https://discuss.hail.is/u/hirbokazi)\ **Replies:** 1\ **Last updated:** [July 13, 2023, 6:13pm UTC](https://discuss.hail.is/t/logistic-regression-using-firth-test-returns-n/3466 "2023-07-13T18:13:58Z")
I am trying to replicate GWAS results for 7 variants that when I perform logistic regression analysis using firth test returns NAs and works fine with linear regression. the sample sizes and MAF are not terrible because … --- ## [Is it possible to remove patches from assembly?](https://discuss.hail.is/t/is-it-possible-to-remove-patches-from-assembly/3411)
**Author:** [@John-Drake](https://discuss.hail.is/u/John-Drake)\ **Replies:** 1\ **Last updated:** [June 1, 2023, 12:54pm UTC](https://discuss.hail.is/t/is-it-possible-to-remove-patches-from-assembly/3411 "2023-06-01T12:54:43Z")
I am using gnomad 3.1.2 to extract SNPs. It is very important that these SNPs align with another customized database containing miRNA sequences. Gnomad documentation on their assembly is weak. From this update, it appea… --- ## [Running polygenic risk scoring with VariantDataset](https://discuss.hail.is/t/running-polygenic-risk-scoring-with-variantdataset/3384)
**Author:** [@karenfeng](https://discuss.hail.is/u/karenfeng)\ **Replies:** 3\ **Last updated:** [May 15, 2023, 4:43pm UTC](https://discuss.hail.is/t/running-polygenic-risk-scoring-with-variantdataset/3384 "2023-05-15T16:43:01Z")
Do you have advice for how to run a polygenic risk score with a VariantDataset? My current flow is taking a painful amount of time to run on the All Of Us short-read WGS dataset and I’m not sure if it’s optimal. vds = h… --- ## [Accessing Blockmatrix data in parallel](https://discuss.hail.is/t/accessing-blockmatrix-data-in-parallel/1948)
**Author:** [@ch283](https://discuss.hail.is/u/ch283)\ **Replies:** 19\ **Last updated:** [April 14, 2023, 3:59pm UTC](https://discuss.hail.is/t/accessing-blockmatrix-data-in-parallel/1948 "2023-04-14T15:59:01Z")
Hi, I have a custom python generator that’s pulling data out of a hail blockmatrix to use for deep learning, as previously discussed here. This has been working pretty well by itself, but when I try to parallelise the d… --- ## [Liftover failure for rs11672691](https://discuss.hail.is/t/liftover-failure-for-rs11672691/3231)
**Author:** [@karenfeng](https://discuss.hail.is/u/karenfeng)\ **Replies:** 3\ **Last updated:** [March 20, 2023, 2:42pm UTC](https://discuss.hail.is/t/liftover-failure-for-rs11672691/3231 "2023-03-20T14:42:34Z")
I’m getting NA when lifting rs11672691 from 19:41985587 on grch37 to grch38, even though it appears to be well-defined: https://www.ncbi.nlm.nih.gov/snp/rs11672691#variant\_details. I’m able to lift 19:41985586 and 19:419… --- ## [Index\_bgen zlib compression exception](https://discuss.hail.is/t/index-bgen-zlib-compression-exception/2652)
**Author:** [@nbaya](https://discuss.hail.is/u/nbaya)\ **Replies:** 9\ **Last updated:** [January 12, 2023, 6:59pm UTC](https://discuss.hail.is/t/index-bgen-zlib-compression-exception/2652 "2023-01-12T18:59:17Z")
I’m trying to index a bgen while on RAP. get\_bgen\_path = lambda chrom: f'file:///mnt/project/Bulk/Exome sequences/Population level exome OQFE variants, BGEN format - interim 450k release/ukb23150\_c{chrom}\_b0\_v1.bgen' ge… --- ## [Case-control imbalance](https://discuss.hail.is/t/case-control-imbalance/3000)
**Author:** [@nafizh](https://discuss.hail.is/u/nafizh)\ **Replies:** 1\ **Last updated:** [December 19, 2022, 7:56pm UTC](https://discuss.hail.is/t/case-control-imbalance/3000 "2022-12-19T19:56:55Z")
I have a dataset that is extremely imbalanced in the case:control ratio. Is there a way to correct for this in hail when running a gwas with the logistic\_regression\_rows() method? Thank you. --- ## [Variant\_qc, AC, AF allele order](https://discuss.hail.is/t/variant-qc-ac-af-allele-order/2997)
**Author:** [@arm](https://discuss.hail.is/u/arm)\ **Replies:** 2\ **Last updated:** [December 16, 2022, 5:48pm UTC](https://discuss.hail.is/t/variant-qc-ac-af-allele-order/2997 "2022-12-16T17:48:16Z")
Hello! Can someone please clarify whether the order of elements in the array at mt.variant\_qc.AC and mt.variant\_qc.AF produced by hl.variant\_qc has any significance? The docs simply say that there is one element for ea… --- ## [Module 'hail.vds' has no attribute 'local\_to\_global'](https://discuss.hail.is/t/module-hail-vds-has-no-attribute-local-to-global/2931)
**Author:** [@Jennifer](https://discuss.hail.is/u/Jennifer)\ **Replies:** 1\ **Last updated:** [October 31, 2022, 11:06pm UTC](https://discuss.hail.is/t/module-hail-vds-has-no-attribute-local-to-global/2931 "2022-10-31T23:06:23Z")
Hello, is there a Hail version restriction on using the function hl.vds.local\_to\_global() (Hail | hail.vds.local\_to\_global)? I’m using 0.2.100 and received an error saying module 'hail.vds' has no attribute 'local\_to\_glo… --- ## [Indel matching in semi\_join/anti\_join](https://discuss.hail.is/t/indel-matching-in-semi-join-anti-join/2902)
**Author:** [@Ruth\_Eberhardt](https://discuss.hail.is/u/Ruth_Eberhardt)\ **Replies:** 2\ **Last updated:** [October 19, 2022, 7:22am UTC](https://discuss.hail.is/t/indel-matching-in-semi-join-anti-join/2902 "2022-10-19T07:22:50Z")
Hi I am using semi\_join(), anti\_join(), semi\_join\_rows() and anti\_join\_rows() to discover variants which are present in both of two datasets, or variants present in only one dataset. I have a question about indel norma… --- ## [De novo calls on hemizygous X variants](https://discuss.hail.is/t/de-novo-calls-on-hemizygous-x-variants/2357)
**Author:** [@Nick](https://discuss.hail.is/u/Nick)\ **Replies:** 20\ **Last updated:** [September 16, 2022, 5:25pm UTC](https://discuss.hail.is/t/de-novo-calls-on-hemizygous-x-variants/2357 "2022-09-16T17:25:49Z")
Hi! I’m using hail’s de novo caller (Hail | Genetics) and I was wondering how it handles hemizygous variants on the X chromosome in males? I’ve used the caller to successfully call DNVs on the X chromosome in females an… --- ## [Obtaining gnomAD allele count data](https://discuss.hail.is/t/obtaining-gnomad-allele-count-data/2834)
**Author:** [@Ruth\_Eberhardt](https://discuss.hail.is/u/Ruth_Eberhardt)\ **Replies:** 2\ **Last updated:** [September 14, 2022, 1:23pm UTC](https://discuss.hail.is/t/obtaining-gnomad-allele-count-data/2834 "2022-09-14T13:23:47Z")
Hi I have downloaded the hail table gs://gcp-public-data–gnomad/release/2.1.1/liftover\_grch38/ht/exomes/gnomad.exomes.r2.1.1.sites.liftover\_grch38.ht (gnomad version 2 exomes lifted over to build 38) and I’d like to ext… --- ## [Implementing fuzzy relational product](https://discuss.hail.is/t/implementing-fuzzy-relational-product/2533)
**Author:** [@garyzhubc](https://discuss.hail.is/u/garyzhubc)\ **Replies:** 0\ **Last updated:** [February 28, 2022, 10:30pm UTC](https://discuss.hail.is/t/implementing-fuzzy-relational-product/2533 "2022-02-28T22:30:23Z")
Is it possible to perform fuzzy relational product with Hail? There are usually two operations, one operate on pairs of entries with a t-norm, another pools the result into one entry through taking the minimum (harsh pro… --- ## [Timeout waiting for connection from pool - loading gVCF from S3](https://discuss.hail.is/t/timeout-waiting-for-connection-from-pool-loading-gvcf-from-s3/2194)
**Author:** [@carleshf](https://discuss.hail.is/u/carleshf)\ **Replies:** 3\ **Last updated:** [November 15, 2021, 10:19am UTC](https://discuss.hail.is/t/timeout-waiting-for-connection-from-pool-loading-gvcf-from-s3/2194 "2021-11-15T10:19:33Z")
Dear all, We are migrating from HDFS to S3 and our previous pipeline is now raising the following error: Java stack trace: org.apache.spark.SparkException: Job aborted due to stage failure: Task 2 in stage 4.0 failed 4… --- ## [Import GLnexus pVCF](https://discuss.hail.is/t/import-glnexus-pvcf/2306)
**Author:** [@poyingfu](https://discuss.hail.is/u/poyingfu)\ **Replies:** 3\ **Last updated:** [October 28, 2021, 7:34pm UTC](https://discuss.hail.is/t/import-glnexus-pvcf/2306 "2021-10-28T19:34:58Z")
Hi Hail team, I’m using GLnexus to joint-call my gvcfs, and I would like to import my pVCF into Hail to do further filtering. But some of GT like “./1”, “./0” will show as NA in Hail. Is there any possible way we can co… --- ## [Modifying variables within hl.agg.linreg](https://discuss.hail.is/t/modifying-variables-within-hl-agg-linreg/2291)
**Author:** [@ajaynadig](https://discuss.hail.is/u/ajaynadig)\ **Replies:** 1\ **Last updated:** [October 13, 2021, 3:22pm UTC](https://discuss.hail.is/t/modifying-variables-within-hl-agg-linreg/2291 "2021-10-13T15:22:12Z")
I am trying to perform linear regression in hail, i.e.: mt = mt.annotate\_cols( lm = hl.agg.linreg(mt.y, \[mt.x1, 1\])) but would like to make a small modification. I have two column fields, a and b, that I wou… --- ## [Bug: n\_alleles may not be missing](https://discuss.hail.is/t/bug-n-alleles-may-not-be-missing/2217)
**Author:** [@Abhishek](https://discuss.hail.is/u/Abhishek)\ **Replies:** 4\ **Last updated:** [September 2, 2021, 2:18pm UTC](https://discuss.hail.is/t/bug-n-alleles-may-not-be-missing/2217 "2021-09-02T14:18:34Z")
Hi, I am testing QC steps and plot generation on a hail matrix table. The QC steps get done but when I try to write the hail matrix to disk, I get the following error: Hail version: 0.2.72-cfce5e858cab Error summary:… --- ## [Trouble downloading public 1000 Genomes data](https://discuss.hail.is/t/trouble-downloading-public-1000-genomes-data/2206)
**Author:** [@mahantesh19](https://discuss.hail.is/u/mahantesh19)\ **Replies:** 1\ **Last updated:** [August 27, 2021, 1:28pm UTC](https://discuss.hail.is/t/trouble-downloading-public-1000-genomes-data/2206 "2021-08-27T13:28:17Z")
I’m trying to follow the tutorial from here: Hail | GWAS Tutorial and I’m getting the following error message: hl.utils.get\_1kg(‘data/’) 2021-08-27 17:20:24 Hail: INFO: downloading 1KG VCF … Source: https://storage.go… --- ## [Looking for specific number of samples in gnomAD 2.1](https://discuss.hail.is/t/looking-for-specific-number-of-samples-in-gnomad-2-1/2188)
**Author:** [@antoine-fav](https://discuss.hail.is/u/antoine-fav)\ **Replies:** 2\ **Last updated:** [August 18, 2021, 7:36am UTC](https://discuss.hail.is/t/looking-for-specific-number-of-samples-in-gnomad-2-1/2188 "2021-08-18T07:36:59Z")
Hello hail users, I am currently working with gnomAD 2.1 exomes and I need to study supposedly “healthy” non-Finnish Europeans samples. I think what I want is the so-called “Controls-only” described here : gnomAD v2.1 |… --- ## [Using Hail for Cohort Querying](https://discuss.hail.is/t/using-hail-for-cohort-querying/1326)
**Author:** [@IqviaGarrettBromley](https://discuss.hail.is/u/IqviaGarrettBromley)\ **Replies:** 5\ **Last updated:** [October 15, 2020, 6:18pm UTC](https://discuss.hail.is/t/using-hail-for-cohort-querying/1326 "2020-10-15T18:18:22Z")
Currently, we have a vast infrastructure for supporting genomic cohort building (which patients have which variants that match a given criteria specified by the user). These systems are built using oracle/hive db/elastic… --- ## [Gwas analyis on whole exome data without controls](https://discuss.hail.is/t/gwas-analyis-on-whole-exome-data-without-controls/1418)
**Author:** [@jotes](https://discuss.hail.is/u/jotes)\ **Replies:** 12\ **Last updated:** [May 30, 2020, 4:35am UTC](https://discuss.hail.is/t/gwas-analyis-on-whole-exome-data-without-controls/1418 "2020-05-30T04:35:49Z")
Hello everybody. My name is Vincent and I have a whole exome sequence data for humans(only one phenotype). I’ll like to know SNPs and loci under selection and if they are unique to our population of study.There was not … [Next page](https://discuss.hail.is/c/science/11.md?page=1)