I am doing imputation using Eagle and it is quite slow. The program gives me a Warning;
> WARNING: --vcfRef does not end in '.bcf'; BCF input is fastest
The command line I am using is;
eagle --vcfRef ref.vcf.gz --vcfTarget target.vcf.gz --geneticMapFile=genetic_map_1cMperMb.txt --chromX=30 --pbwtIters=10 --numThreads=30 --outPrefix=eagle_target_1 --chrom=1
I tried converting my VCF file to BCF format using;
bcftools view target.vcf -Oz -o target.bcf.gz
bcftools index -f target.bcf.gz
but I still get the same warning "--vcfRef does not end in '.bcf'; BCF input is fastest".
Could you please help on where I could be going wrong, I wish to use BCF format if indeed its faster and then later convert to back to VCF. I will also appreciate a code to convert back to VCF from BCF.