eagle: error: argument command: invalid choice: 'DATASET_chr_for_phasing.vcf.gz' (choose from 'interface', 'convert')

I am new to GWAS imputation methods. I am struggling to understand the error while running prephasing step using eagle. Please help me to sort this issue.

My input file dataset is plink generated vcf files containing all chromosoems. Here is command I used from protocols.io () https://www.protocols.io/run/genotype-imputation-workflow-v3-0-xbgfijw?step=9

DATASET=DATASET_chr
# Run phasing for each chromosome
for CHR in {1..22}; do

    # Run phasing for each chromosome separately
    eagle \
           --vcf ${DATASET}_for_phasing.vcf.gz \
           --chrom ${chrname} \
           --geneticMapFile eagle_map_step_1.2.2/eagle_chr${CHR}_b38.map \
           --numThreads=8 \
           --Kpbwt=20000 \
           --outPrefix ${DATASET}_for_imputation_chr${CHR}
done

gwas-imputation

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written 2.0 years ago by nareshmvr •

Are you sure that is the correct option set for eagle?

Eagle manual seems to say

When phasing with a reference panel, Eagle takes input for both the target and reference genotypes in tabix-indexed VCF/BCF format (compressed or uncompressed) using the --vcfTarget and --vcfRef options; the file format is automatically detected. We recommmend using BCF format, as VCF parsing time can be substantial for large data sets

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written 2.0 years ago by GenoMax

Like I mentioned I am following the protocol steps in the link provided. I have seen this manual stating vcfTarget and vcfRef options. Tried as following still same error repeats.

for CHR in {1..23}; do

# Chromosome 23 is coded as 'chrX',
# whereas autosomal chrs are numbers alone
if [ "$CHR" == "23" ]; then
      chrname=chrX
else
      chrname=$CHR
fi


# Run phasing for each chromosome separately
eagle \
       --vcfTarget ${DATASET}_for_phasing.vcf.gz \
       --vcfRef 1000GP_AF_chr${CHR}.vcf.gz
       --chrom ${chrname} \
       --geneticMapFile eagle_map_step_1.2.2/eagle_chr${CHR}_b38.map \
       --numThreads=8 \
       --Kpbwt=20000 \
       --outPrefix ${DATASET}_for_imputation_chr${CHR}

done

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written 2.0 years ago by nareshmvr •

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