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bgzip input.vcf ## this command will produce input.vcf.gz
bgzip input.vcf ## this command will produce input.vcf.gz
tabix -pvcf -f input.vcf.gz ## this command will produce input.vcf.gz.tbi
tabix -pvcf -f input.vcf.gz ## this command will produce input.vcf.gz.tbi
* If the VCF file is separated by chromosome, the VCF file must contain the string "chr1" in the chromosome 1 file, and corresponding chromosome name for other chromosomes.
* If the VCF file is separated by chromosome, the VCF file specified in the input argument must contain the string "chr1" in the chromosome 1 file, and corresponding chromosome name for other chromosomes. Thus, the files names should be like <code>[prefix]chr1[suffix].vcf.gz</code>, <code>[prefix]chr2[suffix].vcf.gz</code>, ..., <code>[prefix]chr22[suffix].vcf.gz</code>, <code>[prefix]chrX[suffix].vcf.gz</code>.
* Sample IDs in the VCF file must be consistent to those from PED file
* Sample IDs in the VCF file must be consistent to those from PED file
* Currently EPACTS only support bi-allelic variants, but it handles SNPs, INDELs, snd SVs.
* Currently EPACTS only support bi-allelic variants, but it handles SNPs, INDELs, snd SVs.
