Question: use gatk phased vcf as input file of HapCut2
gravatar for Peter Chung
20 days 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 • 78 views
ADD COMMENTlink modified 11 days ago by Ram15k • written 20 days 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.

ADD REPLYlink written 11 days ago by Ram15k
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