Hi All,
I try to perform gatk VariantAnnotator, from their website:
VariantAnnotator \
-R reference.fasta \
-I input.bam \
-V input.vcf \
-o output.vcf \
-A Coverage \
--dbsnp dbsnp.vcf
I would like to ask why they may require the bam file for this function? I know that the mandatory field input.vcf already computed from the bam file itself. What may affect if I do not include the bam file?
Best,
1 answer
I would like to ask why they may require the bam file for this function?
hum.. if you want to add the coverage, where do you think gatk can get this information elsewhete than in the bam files ?
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator :
VariantAnnotator \
-R reference.fasta \
-V input.vcf \
-o output.vcf \
--resource:foo resource.vcf \
--expression foo.AF \
--expression foo.FILTER
Log in to answer this question.
-
input for gatk VariantAnnotator --dbsnp
written by QX •
-
GATK 4.3.0 VQSR
written by wonde2000 •
-
dbSNP with RefSeq chromosome notation
written by Tom •
-
Validation of VCF file generated from GATK pipeline
written by Parichitran •
-
Using GATK in conda
written by michael.flower.14 •
-
no variant remained after GenotypeGVCFs gatk4
written by Mehmet
-
How can I call both somatic and germline variants from bam file?
written by svp
-
GATK Mutect2 Panel-Of-Normals generation
written by cocchi.e89
-
ReadPosRankSum annotation error (gatk4)
written by Cricket •
-
Usage of Mutect2
written by gprashant17
