Question: use gatk phased vcf as input file of HapCut2
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gravatar for Peter Chung
3 months ago by
Peter Chung70
Hong Kong
Peter Chung70 wrote:

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.

phasing vcf gatk hapcut2 • 195 views
ADD COMMENTlink modified 3 months ago by Ram17k • written 3 months ago by Peter Chung70

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

ADD REPLYlink written 3 months ago by Ram17k
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