Cargando…
HAT: de novo variant calling for highly accurate short-read and long-read sequencing data
MOTIVATION: de novo variant (DNV) calling is challenging from parent-child sequenced trio data. We developed Hare And Tortoise (HAT) to work as an automated workflow to detect DNVs in highly accurate short-read and long-read sequencing data. Reliable detection of DNVs is important for human genetics...
Autores principales: | , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9900919/ https://www.ncbi.nlm.nih.gov/pubmed/36747667 http://dx.doi.org/10.1101/2023.01.27.525940 |
_version_ | 1784882938143309824 |
---|---|
author | Ng, Jeffrey K. Turner, Tychele N. |
author_facet | Ng, Jeffrey K. Turner, Tychele N. |
author_sort | Ng, Jeffrey K. |
collection | PubMed |
description | MOTIVATION: de novo variant (DNV) calling is challenging from parent-child sequenced trio data. We developed Hare And Tortoise (HAT) to work as an automated workflow to detect DNVs in highly accurate short-read and long-read sequencing data. Reliable detection of DNVs is important for human genetics studies (e.g., autism, epilepsy). RESULTS: HAT is a workflow to detect DNVs from short-read and long read sequencing data. This workflow begins with aligned read data (i.e., CRAM or BAM) from a parent-child sequenced trio and outputs DNVs. HAT detects high-quality DNVs from short-read whole-exome sequencing, short-read whole-genome sequencing, and highly accurate long-read sequencing data. |
format | Online Article Text |
id | pubmed-9900919 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cold Spring Harbor Laboratory |
record_format | MEDLINE/PubMed |
spelling | pubmed-99009192023-02-07 HAT: de novo variant calling for highly accurate short-read and long-read sequencing data Ng, Jeffrey K. Turner, Tychele N. bioRxiv Article MOTIVATION: de novo variant (DNV) calling is challenging from parent-child sequenced trio data. We developed Hare And Tortoise (HAT) to work as an automated workflow to detect DNVs in highly accurate short-read and long-read sequencing data. Reliable detection of DNVs is important for human genetics studies (e.g., autism, epilepsy). RESULTS: HAT is a workflow to detect DNVs from short-read and long read sequencing data. This workflow begins with aligned read data (i.e., CRAM or BAM) from a parent-child sequenced trio and outputs DNVs. HAT detects high-quality DNVs from short-read whole-exome sequencing, short-read whole-genome sequencing, and highly accurate long-read sequencing data. Cold Spring Harbor Laboratory 2023-01-28 /pmc/articles/PMC9900919/ /pubmed/36747667 http://dx.doi.org/10.1101/2023.01.27.525940 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator. |
spellingShingle | Article Ng, Jeffrey K. Turner, Tychele N. HAT: de novo variant calling for highly accurate short-read and long-read sequencing data |
title | HAT: de novo variant calling for highly accurate short-read and long-read sequencing data |
title_full | HAT: de novo variant calling for highly accurate short-read and long-read sequencing data |
title_fullStr | HAT: de novo variant calling for highly accurate short-read and long-read sequencing data |
title_full_unstemmed | HAT: de novo variant calling for highly accurate short-read and long-read sequencing data |
title_short | HAT: de novo variant calling for highly accurate short-read and long-read sequencing data |
title_sort | hat: de novo variant calling for highly accurate short-read and long-read sequencing data |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9900919/ https://www.ncbi.nlm.nih.gov/pubmed/36747667 http://dx.doi.org/10.1101/2023.01.27.525940 |
work_keys_str_mv | AT ngjeffreyk hatdenovovariantcallingforhighlyaccurateshortreadandlongreadsequencingdata AT turnertychelen hatdenovovariantcallingforhighlyaccurateshortreadandlongreadsequencingdata |