Non-model organism more than 23 chromosomes

[197yu]

Hello, my research species is the chicken. How should I adjust the parameters for imputation to accommodate more than 23 chromosomes? Thanks!

[jonathonl]

I don't think any parameters need to be adjusted. Have you encountered any issues?

[197yu]

i run the command follow:
#!/bin/bash
#SBATCH -J minimac3
#SBATCH -p XiaoQingHe
#SBATCH --cpus-per-task=8
#SBATCH --mem=10G
#SBATCH -o minimacchr23.o
#SBATCH -e minimacchr23.e

CHR=23

DIR=./phased/ligated/

mkdir -p $DIR/m3vcf

VCF=F16_phasing/23.phased.vcf.gz

Make m3vcf

Minimac3
--cpus 8 --lowMemory
--refHaps $VCF --processReference --prefix $DIR/m3vcf/chr$CHR

and then i get the error tips follow:

---

      Minimac3 - Fast Imputation Based on State Space Reduction HMM

---

       (c) 2014 - Sayantan Das, Christian Fuchsberger, David Hinds
                         Mary Kate Wing, Goncalo Abecasis 

Version: 2.0.1;
Built: Sat Aug 9 15:45:28 CST 2025 by hxxgroup02

Command Line Options:
Reference Haplotypes : --refHaps [F16_phasing/23.phase.vcf.gz],
--passOnly, --rsid
Target Haplotypes : --haps []
Output Parameters : --prefix [./phased/ligated//m3vcf/chr23],
--processReference [ON], --updateModel, --nobgzip,
--vcfOutput [ON], --doseOutput, --hapOutput,
--format [GT,DS], --allTypedSites
Subset Parameters : --chr [], --start, --end, --window
Starting Parameters : --rec [], --err []
Estimation Parameters : --rounds [5], --states [200]
Other Parameters : --log, --lowMemory [ON], --help, --cpus [8],
--params
PhoneHome : --noPhoneHome, --phoneHomeThinning [50]

URL = http://genome.sph.umich.edu/wiki/Minimac3

NOTE: Since "--processReference" is ON, all options under "Target Haplotypes"
and "Starting Parameters" will be ignored !!!
Program will only estimate parameters and create M3VCF file.
No imputation will be performed, hence other parameters are unnecessary !!!

NOTE: If "--processReference" is ON, Parameter Estimation will be done by default !
Use "--rounds 0" to AVOID Parameter Estimation !!!

Low Memory Version of Minimac3 initiated !!!

---

                       REFERENCE HAPLOTYPE PANEL                           

---

Format = VCF (Variant Call Format)

Loading Reference Haplotype Set from VCF File : F16_phasing/23.phase.vcf.gz

Reading VCF File to calculate number of records ...

Error !!! Reference VCF File contains chromosome : 23
VCF File can only contain chromosomes 1-22 and X !!!
Program Aborting ...

Program Exiting ...

i planed to run the next command to impute my chr23 if i get the file chr23.m3vcf.gz:
minimac4 --update-m3vcf ./phased/ligated/m3vcf/chr1.m3vcf.gz > chr23_reference.msav
minimac4 chr23_reference.msav ./F16_phasing/23.phased.vcf.gz --threads 60 --format GT,HDS,DS,GP,SD --output-format vcf.gz --output ./F16_phasing/F16_chr23_after_imputation2.vcf.gz

[jonathonl]

For parameter estimation with Minimac3, you will have to explicitly specify the chromosome name with --chr. This would be --chr 23 or --chr chr23, depending on what is in the first column of the VCF.

[197yu]

thank you very much !!! help me a lot, the command run successfully!

[197yu]

hello, can i ask you another question? I am using MiniMAC4 for imputation work, and the process is as follows:

1. Process the reference panel, separating chromosomes and phasing, then construct the m3vcf file and convert it into a reference.msav file.
2. Process the population to be imputed. Here, I have obtained the VCF files of the population to be imputed, and I would like to know whether MiniMAC4 imputation directly uses the VCF of the population, or if it is similar to Glimpse2, where you can directly impute based on the individual BAM files which is obtained by mapping individual data (WGS) of the population to the reference genome?
   Thanks for your response!

[jonathonl]

Minimac4 imputes phased VCF files. It does not support BAM files as input.

[197yu]

thanks for your reply! and i want to know could minimac4 impute the SV (structure variation) ,and how should i validate the efficiency and accuracy of imputation by minimac4 for SNP or SV?
i am looking forward for your response!

[jonathonl]

Minimac4 was not designed to impute SVs. It might do an okay job with some types of SVs, but the software has no concept of CNVs for example.

[197yu]

Minimac4 was not designed to impute SVs. It might do an okay job with some types of SVs, but the software has no concept of CNVs for example.

Thanks! I am trying to impute SV (focus on DEL and INS) by minimac4, and i got VCF result of imputation including SNPs and SVs, i did those process where i imitated some articles who impute SVs by Glimpse, and if i can impute SVs efficiently by minimac4, my SV variants resource will be used conveniently, could you give me some advices or do you think the SV imputation mentioned before scientifically？