This is a test version of Biostars. For the public version, visit https://www.biostars.org.
use gatk phased vcf as input file of HapCut2

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.

hapcut2 gatk phasing vcf
• 2,655 views • link
written by Peter Chung Peter Chung

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

• 1 views • link
written by Ram Ram

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

• 0 views • link
written by Peter Chung Peter Chung

0 answers

No answers yet.

Log in to answer this question.

More posts like this