use gatk phased vcf as input file of HapCut2

Question

[Peter Chung]

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 ?

Thank you.

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

[Peter Chung]

hello, did you figure it out which vcf file should be used. I only have one vcf file output from the WGS analysis