WansonChoi/CookHLA

I got error on convert vcf step "Inconsistent marker IDs: [markers file]"

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NeiH4207 commented

[CookHLA.py]: CookHLA : Performing HLA imputation for 'MyHLAImputation/APMDA.samples.phased.COPY.LiftDown_hg18.NoAmbig'

  • Java memory = 8000m(Mb)
  • Using Local Embedding.
  • Using Adaptive Genetic Map.
  • Small Sample mode. (because # of target samples < 100)
    [1] Extracting SNPs from the MHC.
    [2] Performing SNP quality control.
    Warning: 3 variants had at least one non-A/C/G/T allele name.
    Warning: At least 2 duplicate IDs in --exclude file.
    62248
    62248
    62248
    [3] Converting data to beagle format.
    Exception in thread "main" java.lang.IllegalArgumentException: Inconsistent marker IDs: [markers file]=SNPS_DQA1_2481_32639939_intron1 [BEAGLE file]=chr6:32667088:G:A
    at beagleutil.Beagle2Vcf.checkConsistency(Beagle2Vcf.java:153)
    at beagleutil.Beagle2Vcf.main(Beagle2Vcf.java:67)

[HLA_Imputation.py::ERROR]: Input file for imputation('MyHLAImputation/APMDA.samples.51.MHC.QC.vcf') contains nothing. Please check it again.

[HLA_Imputation.py::ERROR]: Input file for imputation('MyHLAImputation/APMDA.samples.51.MHC.QC.vcf') contains nothing. Please check it again.

[HLA_Imputation.py::ERROR]: Input file for imputation('MyHLAImputation/APMDA.samples.51.MHC.QC.vcf') contains nothing. Please check it again.
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