Standard data input - PLINK 2.0
Jan 10, 2026 · To make this more obvious, PLINK 2 now errors out when dosage=GP is used without --import-dosage-certainty on a file with a FORMAT/DS header line, since dosage=DS extracts the …
How to use dosage from Sanger imputation data - Google Groups
Sep 15, 2020 · In the doc it is mentionned that by default dosage is not imported using a vcf and dosage=xx should be used. I imputed my data using Sanger imputation (1000G phase 3).
GitHub - pappewaio/plink2_score_dosage_verification
PLINK2 requires explicit dosage import: Without the dosage=DS flag, PLINK2 defaults to hard call behavior even when dosage information is available in the VCF file.
PLINK: Whole genome data analysis toolset - Harvard University
The --dosage command will take data in a variety of formats (but best suited to BEAGLE-style output, with one SNP per line) potentially compressed and distributed across multiple files, and perform …
plink2 (1) — plink2 — Debian testing — Debian Manpages
Apr 9, 2020 · To import Minimac3-style DS+HDS phased dosage, add 'dosage=HDS'. 'dosage=DS' (or anything else for now) causes the named field to be interpreted as a Minimac3-style dosage. Note …
How to import dosage information to plink binary files?
Nov 5, 2021 · For example, phase and dosage information are currently discarded. (This situation will improve in the future, but we do not have plans to try to handle everything in the file.) Now that I have …
dosage=DS or dosage=HDS? - Google Groups
Oct 2, 2020 · I am running GWAS using plink2 for HRC imputed data (Minimac4). I notice in PLINK2 website, it says “to import Minimac4-style DS+HDS phased dosage, add 'dosage=HDS'. …
TOPMed imputed vcf to plink2 - dosage=DS or HDS - Google Groups
Jul 1, 2022 · After imputation using TOPMed (Michigan server), and to convert vcf to plink2 format should I use dosage=DS or dosage=HDS in the plink2 command ?
for UKB imputed data, should I use "vcf-dosage=DS-force"
Aug 1, 2024 · My question is: should I use DS or DS-force in my command plink2 --pfile --export vcf id-paste=iid bgz vcf-dosage=DS-force? I don't want to accidentally got hardcalls omitted from my output …
can't get dosage to work on plink2 - Google Groups
Mar 24, 2017 · --import-dosage is implemented in the May 7 build (for now, use "plink2 --help import-dosage" to see documentation; I will try to update the online documentation tomorrow night).