# Feature Requests **URL:** https://discuss.hail.is/c/features/7.md [Latest](https://discuss.hail.is/latest.md) · [Categories](https://discuss.hail.is/categories.md) --- ## [About the Feature Requests category](https://discuss.hail.is/t/about-the-feature-requests-category/14)
**Author:** [@hail-team](https://discuss.hail.is/u/hail-team)\ **Replies:** 0
Suggestions for new or improved features. What would make Hail more useful? Suggest a tweak or dream big! The more detail on what and why, the better. If your idea refines an existing topic, please continue the discu… --- ## [SNV De novo calling tool for cohort research at scale](https://discuss.hail.is/t/snv-de-novo-calling-tool-for-cohort-research-at-scale/4251)
**Author:** [@Eliawad14](https://discuss.hail.is/u/Eliawad14)\ **Replies:** 0\ **Last updated:** [June 2, 2026, 3:55pm UTC](https://discuss.hail.is/t/snv-de-novo-calling-tool-for-cohort-research-at-scale/4251 "2026-06-02T15:55:38Z")
My name is Elias and I work in the Genetics Department at Baylor College of Medicine. I created an add on function to the Hail program that can process WGS/WES VCF files for De novo variants in a build-agnostic, pedig… --- ## [Symbolic Alleles and Overlapping Variants](https://discuss.hail.is/t/symbolic-alleles-and-overlapping-variants/4214)
**Author:** [@Mireia](https://discuss.hail.is/u/Mireia)\ **Replies:** 2\ **Last updated:** [December 12, 2025, 9:11am UTC](https://discuss.hail.is/t/symbolic-alleles-and-overlapping-variants/4214 "2025-12-12T09:11:26Z")
Hello! I’ve developed a pipeline using hail that runs QC and calculates stratified AFs fields by sex and ancestry. While working with hl.split\_multi\_hts() and symbolic alleles (\*), I noticed that genotypes are not updat… --- ## [Using GPUs from HAIL](https://discuss.hail.is/t/using-gpus-from-hail/4216)
**Author:** [@jjfarrell](https://discuss.hail.is/u/jjfarrell)\ **Replies:** 1\ **Last updated:** [November 17, 2025, 4:47pm UTC](https://discuss.hail.is/t/using-gpus-from-hail/4216 "2025-11-17T16:47:28Z")
Is it possble to enable the use of GPUs with Hail through the RAPIDS Accelerator for Apache Spark? --- ## [Export MT as PLINK2 pgen/pvar/psam](https://discuss.hail.is/t/export-mt-as-plink2-pgen-pvar-psam/3940)
**Author:** [@DBScan](https://discuss.hail.is/u/DBScan)\ **Replies:** 5\ **Last updated:** [September 3, 2025, 1:32am UTC](https://discuss.hail.is/t/export-mt-as-plink2-pgen-pvar-psam/3940 "2025-09-03T01:32:40Z")
Would it be possible to directly create PLINK2 pgen/pvar/psam from a MatrixTable? The function export\_plink exports only PLINK1 BED/BIM/FAM files. --- ## [Plink\_export of DS value](https://discuss.hail.is/t/plink-export-of-ds-value/4174)
**Author:** [@jjfarrell](https://discuss.hail.is/u/jjfarrell)\ **Replies:** 1\ **Last updated:** [July 15, 2025, 5:30pm UTC](https://discuss.hail.is/t/plink-export-of-ds-value/4174 "2025-07-15T17:30:52Z")
Plink supports converting a VCF file to plink with the GT replaced with the DS value (–export vcf-dosage=DS ) The DS value ,dosage. is generated using TopMed imputation server and is perferred over GT for analysis. Co… --- ## [Adding samples incrementally](https://discuss.hail.is/t/adding-samples-incrementally/85)
**Author:** [@Steven-N-Hart](https://discuss.hail.is/u/Steven-N-Hart)\ **Replies:** 4\ **Last updated:** [February 27, 2025, 5:02pm UTC](https://discuss.hail.is/t/adding-samples-incrementally/85 "2025-02-27T17:02:06Z")
The issue is that all vcfs to be imported have to have the exact same samples in them. This means you have to have all the samples you want to work on inside a single vcf file. Why not just add them incrementally? In ot… --- ## [Transparency (Alpha) in hl.plot.scatter](https://discuss.hail.is/t/transparency-alpha-in-hl-plot-scatter/3678)
**Author:** [@soisa001](https://discuss.hail.is/u/soisa001)\ **Replies:** 0\ **Last updated:** [December 8, 2023, 10:08pm UTC](https://discuss.hail.is/t/transparency-alpha-in-hl-plot-scatter/3678 "2023-12-08T22:08:35Z")
Hello, I am looking to add an alpha parameter to the hl.plot.scatter function. I have PCAs plotted with the scatter function, with many samples (4000+), so I would like to see the overlapping points. Bokeh has an alpha… --- ## [Future support of Elasticsearch version 8](https://discuss.hail.is/t/future-support-of-elasticsearch-version-8/3570)
**Author:** [@souckmi](https://discuss.hail.is/u/souckmi)\ **Replies:** 1\ **Last updated:** [September 5, 2023, 2:08pm UTC](https://discuss.hail.is/t/future-support-of-elasticsearch-version-8/3570 "2023-09-05T14:08:27Z")
Hello everyone, I wanted to ask if the hail.methods.export\_elasticsearch() method will support Elasticsearch version 8 in the near future, since it supports Elasticsearch versions 6.8.x - 7.x.x. according to the documen… --- ## [Support importing phased BGEN files](https://discuss.hail.is/t/support-importing-phased-bgen-files/3558)
**Author:** [@RossDeVito](https://discuss.hail.is/u/RossDeVito)\ **Replies:** 0\ **Last updated:** [August 22, 2023, 10:28pm UTC](https://discuss.hail.is/t/support-importing-phased-bgen-files/3558 "2023-08-22T22:28:22Z")
Hey team, Hail preserves phase information when importing VCF files, but import\_bgen() notes that it does not. Is there something about BGEN files that makes this harder? It would be useful for my current work simulatin… --- ## [Se in logistic 'firth' model](https://discuss.hail.is/t/se-in-logistic-firth-model/3469)
**Author:** [@hirbokazi](https://discuss.hail.is/u/hirbokazi)\ **Replies:** 4\ **Last updated:** [July 11, 2023, 6:30pm UTC](https://discuss.hail.is/t/se-in-logistic-firth-model/3469 "2023-07-11T18:30:17Z")
output from my ‘firth’ model run with command log\_reg = hl.logistic\_regression\_rows( test='firth', y=mt.pheno.trait1, x=mt.GT.n\_alt\_alleles(), covariates=covariates ) does not have standard errors (se… --- ## [Can you support Illumina DRAGEN msVCF?](https://discuss.hail.is/t/can-you-support-illumina-dragen-msvcf/3458)
**Author:** [@lgh2624](https://discuss.hail.is/u/lgh2624)\ **Replies:** 3\ **Last updated:** [July 5, 2023, 8:03am UTC](https://discuss.hail.is/t/can-you-support-illumina-dragen-msvcf/3458 "2023-07-05T08:03:38Z")
Hi all. I’m using DRAGEN to analyze WGS data of about 2,300 probands and their families. Because of the scalability, we conducted joint analysis using iterative gVCF genotyper (IGG) pipeline and I got msVCF as joint ou… --- ## [Interaction Test between SNP \* Covariate for a Binary Outcome](https://discuss.hail.is/t/interaction-test-between-snp-covariate-for-a-binary-outcome/1500)
**Author:** [@jychung](https://discuss.hail.is/u/jychung)\ **Replies:** 7\ **Last updated:** [May 18, 2023, 3:22pm UTC](https://discuss.hail.is/t/interaction-test-between-snp-covariate-for-a-binary-outcome/1500 "2023-05-18T15:22:37Z")
Hello, I found that hail can do interaction test for a continuous outcome using the function, hl.agg.linreg. Can we do the interaction test between snp and covariate for a binary outcome? Thanks, Jaeyoon --- ## [How to capture summarize() outputs?](https://discuss.hail.is/t/how-to-capture-summarize-outputs/3348)
**Author:** [@pbilling](https://discuss.hail.is/u/pbilling)\ **Replies:** 3\ **Last updated:** [April 27, 2023, 6:21pm UTC](https://discuss.hail.is/t/how-to-capture-summarize-outputs/3348 "2023-04-27T18:21:46Z")
Hello, I find the outputs from the summarize() expression incredibly useful for characterizing data and performing coherence checks. How can I capture the output so I can use it programmatically in downstream analyses? … --- ## [Ukbb\_common documentation seems stale](https://discuss.hail.is/t/ukbb-common-documentation-seems-stale/3008)
**Author:** [@VinceCarey](https://discuss.hail.is/u/VinceCarey)\ **Replies:** 12\ **Last updated:** [January 21, 2023, 4:45pm UTC](https://discuss.hail.is/t/ukbb-common-documentation-seems-stale/3008 "2023-01-21T16:45:04Z")
Is the documentation here Hail Format | Pan UKBB susceptible of improvement? Some of the python code is installable via pip, but is it the right code? Should that doc direct the user to installation via pip? The repos… --- ## [Fail to read a T2T VCF](https://discuss.hail.is/t/fail-to-read-a-t2t-vcf/2989)
**Author:** [@VinceCarey](https://discuss.hail.is/u/VinceCarey)\ **Replies:** 8\ **Last updated:** [January 7, 2023, 1:11am UTC](https://discuss.hail.is/t/fail-to-read-a-t2t-vcf/2989 "2023-01-07T01:11:04Z")
Trying to import one of the VCFs found here The risk was high – but the closest reference available is GRCh38 h.init(default\_reference='GRCh38') h.import\_vcf("chr17.genotyped.vcf.gz", force\_bgz=True).write("t2t17.mt") … --- ## [DNARecords integration?](https://discuss.hail.is/t/dnarecords-integration/2820)
**Author:** [@amanas](https://discuss.hail.is/u/amanas)\ **Replies:** 1\ **Last updated:** [September 20, 2022, 8:13pm UTC](https://discuss.hail.is/t/dnarecords-integration/2820 "2022-09-20T20:13:06Z")
Hi @hail-team ! DNARecords has recently been released. It allows exporting a Hail expression into a dataset of tfrecords or parquet files ready to use with machine learning frameworks like Tensorflow or Pytorch. The wh… --- ## [Add option to make scans inclusive](https://discuss.hail.is/t/add-option-to-make-scans-inclusive/2800)
**Author:** [@ch-kr](https://discuss.hail.is/u/ch-kr)\ **Replies:** 2\ **Last updated:** [August 24, 2022, 5:09pm UTC](https://discuss.hail.is/t/add-option-to-make-scans-inclusive/2800 "2022-08-24T17:09:32Z")
Hi hail team! Would it be possible to add an option to make scans inclusive? With this toy example ht: locus transcript observed 1:1 'test' 0 1:2 'test' 1 1:3 'test' 1 1:4 'test2' 1 if I… --- ## [Wilcoxon ranksum test](https://discuss.hail.is/t/wilcoxon-ranksum-test/295)
**Author:** [@konradjk](https://discuss.hail.is/u/konradjk)\ **Replies:** 7\ **Last updated:** [August 19, 2022, 2:43pm UTC](https://discuss.hail.is/t/wilcoxon-ranksum-test/295 "2022-08-19T14:43:44Z")
Any plans for a Wilcoxon ranksum test in the expression language? --- ## [Variant Quality Score Recalibration](https://discuss.hail.is/t/variant-quality-score-recalibration/101)
**Author:** [@jjfarrell](https://discuss.hail.is/u/jjfarrell)\ **Replies:** 3\ **Last updated:** [July 27, 2022, 9:54pm UTC](https://discuss.hail.is/t/variant-quality-score-recalibration/101 "2022-07-27T21:54:24Z")
A hail version of the GATK VQSR Step (Variant Quality Score Recalibration) would be very useful to help scale QC. A variant filter would be updated based on a Guassian Mixture Model rather than on fixed cutoffs of the va… --- ## [Mixed Model support](https://discuss.hail.is/t/mixed-model-support/2766)
**Author:** [@jjfarrell](https://discuss.hail.is/u/jjfarrell)\ **Replies:** 2\ **Last updated:** [July 26, 2022, 5:49pm UTC](https://discuss.hail.is/t/mixed-model-support/2766 "2022-07-26T17:49:46Z")
LinearMixedModel has been dropped with Hail 0.2.94. Are there any future plans for mixed model support? --- ## [Runs of homozygosity](https://discuss.hail.is/t/runs-of-homozygosity/2763)
**Author:** [@ch-kr](https://discuss.hail.is/u/ch-kr)\ **Replies:** 2\ **Last updated:** [July 22, 2022, 4:53pm UTC](https://discuss.hail.is/t/runs-of-homozygosity/2763 "2022-07-22T16:53:14Z")
Hi hail team! It would be super helpful for QC to have a metric that measures contiguous runs of homozgyosity. This would be useful in our relatedness inference to differentiate between technical artifacts and samples w… --- ## [Window\_by\_locus not available](https://discuss.hail.is/t/window-by-locus-not-available/2716)
**Author:** [@EnQu](https://discuss.hail.is/u/EnQu)\ **Replies:** 2\ **Last updated:** [June 20, 2022, 6:55am UTC](https://discuss.hail.is/t/window-by-locus-not-available/2716 "2022-06-20T06:55:17Z")
Hello there, I just recently discovered Hail from the Nat. Comm. paper 2020 about annotation of MNVs. I tried to followed the tutorials on how to identify and annotate potential MNVs from a VCF file. However, the funct… --- ## [Annotating with CADD, gnomad, Clinvar & dbNSFP on UKB RAP](https://discuss.hail.is/t/annotating-with-cadd-gnomad-clinvar-dbnsfp-on-ukb-rap/2654)
**Author:** [@dint](https://discuss.hail.is/u/dint)\ **Replies:** 7\ **Last updated:** [May 25, 2022, 1:56pm UTC](https://discuss.hail.is/t/annotating-with-cadd-gnomad-clinvar-dbnsfp-on-ukb-rap/2654 "2022-05-25T13:56:55Z")
i’m just wondering if you can specify cadd, gnomad, clinvar and dbNSFP options when annotating with hail on dxjupyterlab\_spark\_cluster o the UKB RAP? From the hail website, the following command can be used on your matri… --- ## [Extract sequence from reference genome](https://discuss.hail.is/t/extract-sequence-from-reference-genome/2670)
**Author:** [@jjfarrell](https://discuss.hail.is/u/jjfarrell)\ **Replies:** 2\ **Last updated:** [May 17, 2022, 6:59pm UTC](https://discuss.hail.is/t/extract-sequence-from-reference-genome/2670 "2022-05-17T18:59:24Z")
Is there a way to extract a slice of the Hail reference genome? rg = hl.get\_reference(‘GRCh38’) seq=rg.seq(chr19:44905796-44909393) For SV calls, the ref and alt are often not the sequence but instead place holders DE… --- ## [How to suppress hail info output](https://discuss.hail.is/t/how-to-suppress-hail-info-output/2596)
**Author:** [@Teculos](https://discuss.hail.is/u/Teculos)\ **Replies:** 2\ **Last updated:** [April 11, 2022, 12:44am UTC](https://discuss.hail.is/t/how-to-suppress-hail-info-output/2596 "2022-04-11T00:44:55Z")
Hello - Is there a way to mute the hail console output when calling functions such as .to\_pandas() or .collect()? I was expecting there to be a verbose parameter for these functions to control that but there doesn’t appe… --- ## [SNP Eff Annotation](https://discuss.hail.is/t/snp-eff-annotation/2546)
**Author:** [@jjfarrell](https://discuss.hail.is/u/jjfarrell)\ **Replies:** 2\ **Last updated:** [March 23, 2022, 2:59pm UTC](https://discuss.hail.is/t/snp-eff-annotation/2546 "2022-03-23T14:59:35Z")
Could an annotation module using snpEff be implemented in Hail? We find it runs faster than VEP and much easier to install. The software is found here:SnpEff and SnpSift --- ## [\[PRS analysis\] Request for allele frequency harmonization and SNP matching features](https://discuss.hail.is/t/prs-analysis-request-for-allele-frequency-harmonization-and-snp-matching-features/2414)
**Author:** [@soo](https://discuss.hail.is/u/soo)\ **Replies:** 2\ **Last updated:** [December 20, 2021, 8:53am UTC](https://discuss.hail.is/t/prs-analysis-request-for-allele-frequency-harmonization-and-snp-matching-features/2414 "2021-12-20T08:53:58Z")
Hi all, I am working on PRS analysis these days and have some feature requests regarding SNP matching of the target data and GWAS summary statistics. Allele frequency harmonization: When matching SNPs, I want to harm… --- ## [ABHet ratio for variant level QC](https://discuss.hail.is/t/abhet-ratio-for-variant-level-qc/2258)
**Author:** [@jjfarrell](https://discuss.hail.is/u/jjfarrell)\ **Replies:** 4\ **Last updated:** [September 22, 2021, 3:35pm UTC](https://discuss.hail.is/t/abhet-ratio-for-variant-level-qc/2258 "2021-09-22T15:35:21Z")
A very useful metric for variant QC is the ABHet ratio. Variants with ABHet \< 0.2 and \> 0.8 are used to filter out false positives. More conservative cutoffs (0.25 and 0.75) are also used. ABHet is a variant-level an… --- ## [Implement Regenie](https://discuss.hail.is/t/implement-regenie/2168)
**Author:** [@inninun](https://discuss.hail.is/u/inninun)\ **Replies:** 3\ **Last updated:** [August 26, 2021, 7:07am UTC](https://discuss.hail.is/t/implement-regenie/2168 "2021-08-26T07:07:56Z")
Hi Hail team, Regenie is for the gene/region-based burden test and it works on both quantitative and binary traits. It would be very useful for whole-genome regression modeling. I would be very happy if Regenie could b… [Next page](https://discuss.hail.is/c/features/7.md?page=1)