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Santy-8128 / Minimac3

Minimac3 is a low memory and computationally efficient implementation of the genotype imputation algorithms. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
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Error with hg38 aligned vcf file #10

Open jjfarrell opened 6 years ago

jjfarrell commented 6 years ago

When running processReference on a hg38 aligned reference, the following error occurs. Minimac3 does not seem to like chr1-chr22 and is expecting 1-22. What is the best way to handle hg38 aligned vcf files?

--------------------------------------------------------------------------------
          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: Wed Nov 30 11:30:06 EST 2016 by cjahnke

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

 Command Line Options:
    Reference Haplotypes : --refHaps [pVCF.4794.panel/adsp-5k.hg38.GATK.aws-batch_SNP_INDEL.chr19.4794samples.phased.vcf.gz],
                           --passOnly, --rsid
       Target Haplotypes : --haps []
       Output Parameters : --prefix [m3vcf/adsp-5k.chr19],
                           --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, --help, --cpus [1], --params
               PhoneHome : --noPhoneHome, --phoneHomeThinning [50]

 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 !!!

 ------------------------------------------------------------------------------
                           REFERENCE HAPLOTYPE PANEL
 ------------------------------------------------------------------------------

 Format = VCF (Variant Call Format)

 Loading Reference Haplotype Set from VCF File       : pVCF.4794.panel/adsp-5k.hg38.GATK.aws-batch_SNP_INDEL.chr19.4794samples.phased.vcf.gz

 Reading VCF File to calculate number of records ...

 Error !!! Reference VCF File contains chromosome : chr19
 VCF File can only contain chromosomes 1-22 and X !!!
 Program Aborting ...

 Program Exiting ...
Santy-8128 commented 6 years ago

You can use --myChromosome chr20

It is a latent parameter. Please let me know if that doesn't work.

Regards, Sayantan Das,

23andMe

On Mon, Jul 23, 2018 at 9:03 AM jjfarrell notifications@github.com wrote:

When running processReference on a hg38 aligned reference, the following error occurs. Minimac3 does not seem to like chr1-chr22 and is expecting 1-22. What is the best way to handle hg38 aligned vcf files?

      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: Wed Nov 30 11:30:06 EST 2016 by cjahnke

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

Command Line Options: Reference Haplotypes : --refHaps [pVCF.4794.panel/adsp-5k.hg38.GATK.aws-batch_SNP_INDEL.chr19.4794samples.phased.vcf.gz], --passOnly, --rsid Target Haplotypes : --haps [] Output Parameters : --prefix [m3vcf/adsp-5k.chr19], --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, --help, --cpus [1], --params PhoneHome : --noPhoneHome, --phoneHomeThinning [50]

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 !!!

                       REFERENCE HAPLOTYPE PANEL

Format = VCF (Variant Call Format)

Loading Reference Haplotype Set from VCF File : pVCF.4794.panel/adsp-5k.hg38.GATK.aws-batch_SNP_INDEL.chr19.4794samples.phased.vcf.gz

Reading VCF File to calculate number of records ...

Error !!! Reference VCF File contains chromosome : chr19 VCF File can only contain chromosomes 1-22 and X !!! Program Aborting ...

Program Exiting ...

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