Speeding up Eagle phasing and imputation
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.
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