I am new in sequencing analysis and would like to do haplotype blocks from the result of WGS. But I have some questions on the HAPCUT2.
I generated a vcf from gatk and then I phased it using gatk ReadBackedPhasing into phased vcf.
Commands below are from HAPCUT2:
./build/extractHAIRS [options] --bam reads.sorted.bam --VCF variants.VCF --out fragment_file ./build/HAPCUT2 --fragments fragment_file --vcf variantcalls.vcf --output haplotype_output_file
I saw there are two vcf files in different names, so which one should I input my phased vcf and what is another vcf file ? btw, is it better to put a phased vcf in HAPCUT2 ?