HaplotypeCaller GVCF on one bam files

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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

variant calling GATK HaplotypeCaller • 1.3k views

ADD COMMENT • link 3.4 years ago by rayzghimire • 0

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gvcf is effective while calling variants on a cohort of bam files. Is that correct?

yes

ADD REPLY • link 3.4 years ago by Pierre Lindenbaum 161k

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Hi Pierre, So should I use genotypeCalling for a single gvcf file? How is it different from the vcf generated by HaplotypeCaller?

Thank you

ADD REPLY • link 3.4 years ago by rayzghimire • 0

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you just call HaplotypeCaller without -ERC GVCF and you'll get a standard vcf

ADD REPLY • link 3.4 years ago by Pierre Lindenbaum 161k

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