Question: [gatk 3.6.0] GVCF - haplotypecaller - cross referencing multiple VCF
0
gravatar for agamemnon
4 months ago by
agamemnon0
agamemnon0 wrote:

Hi there,

how do you make a GVCF file from bam files, using [gatk 3.6] haplotypecaller if wanting to compare patient with their two parents?

I have three vcf files, but no gvcf files. I would like to be able to compare de novo as well as inherited variants. Are there any alternative processes apart from using GATK [3.6.0] GenotypeGVCF, followed by SelectVariants and then running the annotation software/database?

Thanks

Aga

gvcf vcf haplotypecaller • 139 views
ADD COMMENTlink written 4 months ago by agamemnon0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 867 users visited in the last hour