# Hail Query & hailctl **URL:** https://discuss.hail.is/c/help-02/16.md?page=1 [Latest](https://discuss.hail.is/latest.md) · [Categories](https://discuss.hail.is/categories.md) **Page:** 2 --- ## [Socketexpection network is unreachable - hail read matrix table](https://discuss.hail.is/t/socketexpection-network-is-unreachable-hail-read-matrix-table/4160)
**Author:** [@complexgenome](https://discuss.hail.is/u/complexgenome)\ **Replies:** 0\ **Last updated:** [June 5, 2025, 3:57pm UTC](https://discuss.hail.is/t/socketexpection-network-is-unreachable-hail-read-matrix-table/4160 "2025-06-05T15:57:45Z")
Hi there, I am trying to run hail gnomad tutorial for ancestry. It is convulated for my skills. I have installed all tools, dependencies, set jar path and other things. import sys print(sys.path) sys.path.append(‘/… --- ## [No FileSystem for scheme "gs" - gnomad](https://discuss.hail.is/t/no-filesystem-for-scheme-gs-gnomad/4135)
**Author:** [@complexgenome](https://discuss.hail.is/u/complexgenome)\ **Replies:** 6\ **Last updated:** [June 5, 2025, 3:52pm UTC](https://discuss.hail.is/t/no-filesystem-for-scheme-gs-gnomad/4135 "2025-06-05T15:52:36Z")
Hi there, I’m struggling hard with hail, gnomad pipeline for ancestry estimation. When I run following code with hl.hadoop\_open(gnomad\_v3\_onnx\_rf, “rb”) as f: v3\_onx\_fit = onnx.load(f) I run into error on python jup… --- ## [How access Neale Lab genetic correlation browser?](https://discuss.hail.is/t/how-access-neale-lab-genetic-correlation-browser/1399)
**Author:** [@crespi](https://discuss.hail.is/u/crespi)\ **Replies:** 3\ **Last updated:** [June 5, 2025, 10:17am UTC](https://discuss.hail.is/t/how-access-neale-lab-genetic-correlation-browser/1399 "2025-06-05T10:17:49Z")
Hi I am new to Hail. Might I please ask how I might access the Neale Lab genetic correlation browser? I can find the heritability browser but not the genetic correlation one. Alternatively, I have downloaded the full… --- ## [Query planner best practices](https://discuss.hail.is/t/query-planner-best-practices/4154)
**Author:** [@pettyalex](https://discuss.hail.is/u/pettyalex)\ **Replies:** 0\ **Last updated:** [May 28, 2025, 10:29pm UTC](https://discuss.hail.is/t/query-planner-best-practices/4154 "2025-05-28T22:29:22Z")
Hello, I’m trying to understand how to help the query planner perform better on large datasets, as well as how to scale clusters effectively. I have a dataset that’s (73494807, 250115) in size, with about 250k whole gen… --- ## [How VDS handles missing data?](https://discuss.hail.is/t/how-vds-handles-missing-data/4149)
**Author:** [@zengchenjie](https://discuss.hail.is/u/zengchenjie)\ **Replies:** 2\ **Last updated:** [May 27, 2025, 6:57pm UTC](https://discuss.hail.is/t/how-vds-handles-missing-data/4149 "2025-05-27T18:57:28Z")
I wonder if missing/unstored calls are assumed to be homozygous reference unless otherwise specified in VDS format. Thanks. --- ## [Hail for GEL .bgen import in UKB RAP](https://discuss.hail.is/t/hail-for-gel-bgen-import-in-ukb-rap/4145)
**Author:** [@albbaous07](https://discuss.hail.is/u/albbaous07)\ **Replies:** 0\ **Last updated:** [May 26, 2025, 11:58am UTC](https://discuss.hail.is/t/hail-for-gel-bgen-import-in-ukb-rap/4145 "2025-05-26T11:58:04Z")
Hi all, I am trying to compute info scores using HAIL in the UKB RAP and GEL imputed .bgen files which are zstd compressed. I am doing this in the HAIL-VEP feature of ukb. I am trying to follow this github doc on import… --- ## [Export bgen from VDS for 14 million variants and 414k samples of AoU](https://discuss.hail.is/t/export-bgen-from-vds-for-14-million-variants-and-414k-samples-of-aou/4143)
**Author:** [@Arshiya\_Fathima](https://discuss.hail.is/u/Arshiya_Fathima)\ **Replies:** 0\ **Last updated:** [May 26, 2025, 9:14am UTC](https://discuss.hail.is/t/export-bgen-from-vds-for-14-million-variants-and-414k-samples-of-aou/4143 "2025-05-26T09:14:44Z")
Hi team ! Asking for some insights/tips I have filtered around 14 million variants for 414k samples in chr6 of AoU from VDS and trying to export it into .bgen format… The code snippets is as follows: mt\_bgen = mt\_pli… --- ## [How to extract sample IDs from MT](https://discuss.hail.is/t/how-to-extract-sample-ids-from-mt/4141)
**Author:** [@alan.dimitriev](https://discuss.hail.is/u/alan.dimitriev)\ **Replies:** 0\ **Last updated:** [May 25, 2025, 12:32am UTC](https://discuss.hail.is/t/how-to-extract-sample-ids-from-mt/4141 "2025-05-25T00:32:15Z")
Hello, I am trying to use HAIL to quickly annotate VCF files using VEP/LOFTEE and filter for LOF variant carriers. My code works great up until I need to extract the Subject IDs from the MT and then I have faced a host … --- ## [How to use impute\_sex() on a run\_combiner() sparse MatrixTable?](https://discuss.hail.is/t/how-to-use-impute-sex-on-a-run-combiner-sparse-matrixtable/2083)
**Author:** [@antoniocampos13](https://discuss.hail.is/u/antoniocampos13)\ **Replies:** 5\ **Last updated:** [May 21, 2025, 11:59am UTC](https://discuss.hail.is/t/how-to-use-impute-sex-on-a-run-combiner-sparse-matrixtable/2083 "2025-05-21T11:59:48Z")
Hello! I have been struggling to make impute\_sex() work as expected. A few days ago, I was having problems with run\_combiner(), but I finally got it to work with my gVCFs by updating to Hail version 0.2.67. Now, reading … --- ## [Split multi: index out of bound on chrX - LPL column](https://discuss.hail.is/t/split-multi-index-out-of-bound-on-chrx-lpl-column/3349)
**Author:** [@gameforcela12](https://discuss.hail.is/u/gameforcela12)\ **Replies:** 2\ **Last updated:** [May 21, 2025, 11:53am UTC](https://discuss.hail.is/t/split-multi-index-out-of-bound-on-chrx-lpl-column/3349 "2025-05-21T11:53:50Z")
Hello I am working with VariantDataset and I want to use vds = hl.vds.split\_multi(vds) It works ok, but I have problem with chrX with LPL entries. When I split multi on chrX the following error shows up: Error summary… --- ## [Efficient GWAS analyses: expected time and resources](https://discuss.hail.is/t/efficient-gwas-analyses-expected-time-and-resources/4137)
**Author:** [@gsgarlata](https://discuss.hail.is/u/gsgarlata)\ **Replies:** 0\ **Last updated:** [May 21, 2025, 4:43am UTC](https://discuss.hail.is/t/efficient-gwas-analyses-expected-time-and-resources/4137 "2025-05-21T04:43:04Z")
I am trying to run GWAS with one trait, including about 400K individuals, and the UKB imputation dataset (code 22828) using Hail . I am running my analysis with the dx run app-dxjupyterlab\_spark\_cluster command in the UK… --- ## [Ancestry Estimation for many VCFs](https://discuss.hail.is/t/ancestry-estimation-for-many-vcfs/4136)
**Author:** [@Pinegraphite123](https://discuss.hail.is/u/Pinegraphite123)\ **Replies:** 0\ **Last updated:** [May 21, 2025, 4:18am UTC](https://discuss.hail.is/t/ancestry-estimation-for-many-vcfs/4136 "2025-05-21T04:18:01Z")
Hi there, I have a working code that takes one germline variant vcf. Now I want to make it take multiple vcf files and project them all onto the PCA plot and generate a table which simple store sample ID and prediction… --- ## [Pip install hail error - import datetime](https://discuss.hail.is/t/pip-install-hail-error-import-datetime/4133)
**Author:** [@complexgenome](https://discuss.hail.is/u/complexgenome)\ **Replies:** 1\ **Last updated:** [May 20, 2025, 3:04pm UTC](https://discuss.hail.is/t/pip-install-hail-error-import-datetime/4133 "2025-05-20T15:04:16Z")
Hi there, I created a conda env to work with gnomad libraries. I then installed pip in the conda env. When I try to install hail I get a long trace back error. It originates as ImportError: PyCapsule\_Import could n… --- ## [UK Biobank DRAGEN WGS BGEN files use 16-bit probabilities that are incompatible with Hail](https://discuss.hail.is/t/uk-biobank-dragen-wgs-bgen-files-use-16-bit-probabilities-that-are-incompatible-with-hail/4108)
**Author:** [@andrewmagis](https://discuss.hail.is/u/andrewmagis)\ **Replies:** 4\ **Last updated:** [May 12, 2025, 2:13pm UTC](https://discuss.hail.is/t/uk-biobank-dragen-wgs-bgen-files-use-16-bit-probabilities-that-are-incompatible-with-hail/4108 "2025-05-12T14:13:49Z")
WGS DRAGEN BGEN files were recently released on UKBB. Using HAIL 2.4 1 on a Spark cluster, I generated Hail index files using the following command in Python: hl.index\_bgen(path=file\_url, index\_file\_map={f… --- ## [Error while copying genebass on ukb-rap](https://discuss.hail.is/t/error-while-copying-genebass-on-ukb-rap/4127)
**Author:** [@mgota](https://discuss.hail.is/u/mgota)\ **Replies:** 0\ **Last updated:** [May 9, 2025, 10:02pm UTC](https://discuss.hail.is/t/error-while-copying-genebass-on-ukb-rap/4127 "2025-05-09T22:02:20Z")
Error - Hail version: 0.2.132-678e1f52b999 Error summary: GoogleJsonResponseException: 400 Bad Request GET https://storage.googleapis.com/storage/v1/b/ukbb-exome-public/o/500k%2Fresults%2Fvariant\_results.mt%2Fmetadata.… --- ## [VEP Annotation stalling](https://discuss.hail.is/t/vep-annotation-stalling/4125)
**Author:** [@rjanan](https://discuss.hail.is/u/rjanan)\ **Replies:** 0\ **Last updated:** [May 9, 2025, 3:17pm UTC](https://discuss.hail.is/t/vep-annotation-stalling/4125 "2025-05-09T15:17:26Z")
I am running Hail locally and im trying to annotate my MatrixTable with VEP but it keeps stalling. I am testing it on a full dataset with whole exome sequencing of 400 samples and also a small subset of 5 variants with 1… --- ## [Writing my table as csv or vcf or ht takes too long](https://discuss.hail.is/t/writing-my-table-as-csv-or-vcf-or-ht-takes-too-long/4086)
**Author:** [@Hanin\_Omar](https://discuss.hail.is/u/Hanin_Omar)\ **Replies:** 5\ **Last updated:** [May 4, 2025, 5:51am UTC](https://discuss.hail.is/t/writing-my-table-as-csv-or-vcf-or-ht-takes-too-long/4086 "2025-05-04T05:51:18Z")
My scripts is supposed to search for a list of variants in gnomad database using hail, and only retrieve the variants that matched if the exome\_AF filed is \<= 1%, however the bottleneck of the code is the exporting proce… --- ## [Arithmetic errors with casting between floats and ints](https://discuss.hail.is/t/arithmetic-errors-with-casting-between-floats-and-ints/4119)
**Author:** [@Christopher\_Kachulis](https://discuss.hail.is/u/Christopher_Kachulis)\ **Replies:** 2\ **Last updated:** [April 30, 2025, 3:48pm UTC](https://discuss.hail.is/t/arithmetic-errors-with-casting-between-floats-and-ints/4119 "2025-04-30T15:48:24Z")
this is on version 0.2.130.post1-c69cd67afb8b it seems that in some scenarios, casting back and forth between ints and floats can create arithmetic errors, presumably due to some error occurring during the casting. min… --- ## [Parsing results from regression on multiple phenotypes](https://discuss.hail.is/t/parsing-results-from-regression-on-multiple-phenotypes/4115)
**Author:** [@sservice2003](https://discuss.hail.is/u/sservice2003)\ **Replies:** 0\ **Last updated:** [April 25, 2025, 10:16pm UTC](https://discuss.hail.is/t/parsing-results-from-regression-on-multiple-phenotypes/4115 "2025-04-25T22:16:48Z")
Hi - hail newbie here. I am trying to run linear regression on 8 phenotypes. They can be arranged into 4 sets of 2 each, where each set of 2 has the same missingness structure. My code is: lin\_reg = hl.linear\_regress… --- ## [Hl.export\_plink taking too long](https://discuss.hail.is/t/hl-export-plink-taking-too-long/4112)
**Author:** [@Jing\_Zhang](https://discuss.hail.is/u/Jing_Zhang)\ **Replies:** 0\ **Last updated:** [April 23, 2025, 8:57pm UTC](https://discuss.hail.is/t/hl-export-plink-taking-too-long/4112 "2025-04-23T20:57:57Z")
Hi, I have a plink binary file (.bed,.bim,.fam) that is on GRCh38 and I am trying to use hail to liftover it to GRCh37. The .bed file is about 25GB. There are 71267 samples and 1414695 variants. I used mt = hl.methods.… --- ## [Variant Annotation Table Merge?](https://discuss.hail.is/t/variant-annotation-table-merge/4069)
**Author:** [@Cecile\_Avery](https://discuss.hail.is/u/Cecile_Avery)\ **Replies:** 2\ **Last updated:** [April 15, 2025, 11:52pm UTC](https://discuss.hail.is/t/variant-annotation-table-merge/4069 "2025-04-15T23:52:17Z")
Hello, I am supporting a project using All of Us genomic data, which has opted to store their data in hail matrix tables (and other formats). To reduce the file size, they have separated variant annotations in a separa… --- ## [Manhattan plot not showing up](https://discuss.hail.is/t/manhattan-plot-not-showing-up/4083)
**Author:** [@njain](https://discuss.hail.is/u/njain)\ **Replies:** 5\ **Last updated:** [April 15, 2025, 11:49pm UTC](https://discuss.hail.is/t/manhattan-plot-not-showing-up/4083 "2025-04-15T23:49:43Z")
Hi all, I don’t know why the manhattan plot is not showing up for my analysis. For reference, my matrix table dimensions are (8401, 75). I want to do the manhattan plot based on age just in one chromosomal region. Here… --- ## [Split\_multi\_hts altering GQs](https://discuss.hail.is/t/split-multi-hts-altering-gqs/4102)
**Author:** [@Ruth\_Eberhardt](https://discuss.hail.is/u/Ruth_Eberhardt)\ **Replies:** 0\ **Last updated:** [April 8, 2025, 12:58pm UTC](https://discuss.hail.is/t/split-multi-hts-altering-gqs/4102 "2025-04-08T12:58:51Z")
Hi When running split\_multi\_hts on a matrixtable I am finding GQs are being changed, can someone explain this behaviour to me. I am happy to provide VCF and jupyter notebook for the below if you can advise me on how to… --- ## [Exporting Hail MT to VCF - FORMAT columns missing](https://discuss.hail.is/t/exporting-hail-mt-to-vcf-format-columns-missing/4076)
**Author:** [@Lnizz\_b](https://discuss.hail.is/u/Lnizz_b)\ **Replies:** 3\ **Last updated:** [March 31, 2025, 4:42pm UTC](https://discuss.hail.is/t/exporting-hail-mt-to-vcf-format-columns-missing/4076 "2025-03-31T16:42:55Z")
Hello, I am new to Hail and am exporting a Hail MT to VCF using the All of Us code snippets; the code runs fine however the FORMAT columns are omitted despite the necessary entry fields being present in the MatrixTable.… --- ## [Clarification on Linear Model in Hail: genetic relatedness and covariate](https://discuss.hail.is/t/clarification-on-linear-model-in-hail-genetic-relatedness-and-covariate/4091)
**Author:** [@gsgarlata](https://discuss.hail.is/u/gsgarlata)\ **Replies:** 0\ **Last updated:** [March 28, 2025, 5:23pm UTC](https://discuss.hail.is/t/clarification-on-linear-model-in-hail-genetic-relatedness-and-covariate/4091 "2025-03-28T17:23:01Z")
I am performing GWAS on simulated data following this tutorial Hail | GWAS Tutorial. In particular: hl.import\_plink(bed = InputFile + '.bed', bim = InputFile + '.bim', fam = InputFile + '.fam', quant\_pheno = True).writ… --- ## [Inbreeding coefficient function in Hail](https://discuss.hail.is/t/inbreeding-coefficient-function-in-hail/4078)
**Author:** [@CuriousGeneticist](https://discuss.hail.is/u/CuriousGeneticist)\ **Replies:** 1\ **Last updated:** [March 24, 2025, 1:43pm UTC](https://discuss.hail.is/t/inbreeding-coefficient-function-in-hail/4078 "2025-03-24T13:43:28Z")
Hi all! I am just wondering if any of you know if there is an in-built function in Hail to calculate inbreeding coefficient from a MatrixTable. Thanks! --- ## [Trying to annotate vcf subset and then filter according to properties](https://discuss.hail.is/t/trying-to-annotate-vcf-subset-and-then-filter-according-to-properties/4073)
**Author:** [@c.clarkson](https://discuss.hail.is/u/c.clarkson)\ **Replies:** 9\ **Last updated:** [March 21, 2025, 7:25pm UTC](https://discuss.hail.is/t/trying-to-annotate-vcf-subset-and-then-filter-according-to-properties/4073 "2025-03-21T19:25:23Z")
Hello I am new to Hail please forgive my ignorance. I am using the UKBB and hail seems really difficult to use and yet the only possible way to complete the following: I need to isolate a locus within a very large VCF … --- ## [Gentoype filtering - missing hom ref data](https://discuss.hail.is/t/gentoype-filtering-missing-hom-ref-data/4071)
**Author:** [@Mireia](https://discuss.hail.is/u/Mireia)\ **Replies:** 2\ **Last updated:** [March 20, 2025, 11:21am UTC](https://discuss.hail.is/t/gentoype-filtering-missing-hom-ref-data/4071 "2025-03-20T11:21:10Z")
Hello! I’m using hail for a quality control pipeline. I transform a VCF into a hail matrix, run the quality control and then export it as a VCF again. I’ve noticed that after filtering the gentotypes the reference geno… --- ## [Exporting Hail MT to VCF - Missing Genotypes](https://discuss.hail.is/t/exporting-hail-mt-to-vcf-missing-genotypes/3823)
**Author:** [@jasmussen](https://discuss.hail.is/u/jasmussen)\ **Replies:** 11\ **Last updated:** [May 8, 2024, 3:29pm UTC](https://discuss.hail.is/t/exporting-hail-mt-to-vcf-missing-genotypes/3823 "2024-05-08T15:29:31Z")
Hi – I am working in the Hail exome matrix table in the All of Us biobank. Once I subset the MT for my cohort of interest, I have been exporting to VCF. This is for a couple of reasons, but mainly b/c the algorithms use… --- ## [Could not convert string to float: '1,00000e+00'](https://discuss.hail.is/t/could-not-convert-string-to-float-1-00000e-00/1384)
**Author:** [@RezValeri](https://discuss.hail.is/u/RezValeri)\ **Replies:** 3\ **Last updated:** [March 12, 2025, 1:42am UTC](https://discuss.hail.is/t/could-not-convert-string-to-float-1-00000e-00/1384 "2025-03-12T01:42:35Z")
Hello, while doing QQ plot faced with problem - ValueError: could not convert string to float: ‘1,00000e+00’ But manhattan plot is ok. What should I do? The whole error looks this: ValueError … [Previous page](https://discuss.hail.is/c/help-02/16.md) [Next page](https://discuss.hail.is/c/help-02/16.md?page=2)