Entering edit mode
3.4 years ago
rayzghimire
•
0
Hi Guys, I have two fastq files for a single patient. They have paired-end reads. I am using Haplotype caller to generate variants. So while generating the variants should I Just generate vcf directly from haplotype caller or a gvcf and then use genotype calling. From my understanding gvcf is effective while calling variants on a cohort of bam files. Is that correct?
Thank you
yes
Hi Pierre, So should I use genotypeCalling for a single gvcf file? How is it different from the vcf generated by HaplotypeCaller?
Thank you
you just call HaplotypeCaller without
-ERC GVCF
and you'll get a standard vcf