More posts like this
-
Variant calling using HaplotypeCaller does not show #FILTER information
written by QX •
-
Calling zero mapping quality variant
written by sonsunjirachote •
-
Error with Gatk Haplotypecaller
written by Sowmya Pulapet •
-
How to extract region from GVCF file?
written by optimistsso4co3 •
-
gVCF size human genome
written by quentin54520 •
-
GATK HaplotypeCaller Error
written by julianneradford •
-
GATK gvcf file header [ALT=<ID=NON_REF]
written by BioRyder
-
How to force GATK haplotypecaller to output all genomic position (even non variant positions)
written by Nicolas Rosewick
-
Error: Could not find or load main class -Xmx4g
written by Adriel Rosa •
-
gVCF from VCF and BAM
written by tejaswikoganti
More details, I made gvcf file in the following step.
using sort bam file as a input -> gatk4 Baserecalibration -> gatk4 ApplyBQSR -> gatk4 HalotypeCaller -ERC GVCF -> gvcf file
thanks,
What do you want to do with the BAM file that you would get from the "gvcf -> BAM conversion"? I mean you are using a BAM file as the input of the whole pipeline. Cant you use that one to do whatever you want to do?
I wanted to make a bam file for using another varinat call tools.
sounds like "Can I get a cow from a steack ?"
Thank you for your answer. I understand that it is impossible if your posting is appropriate.