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5 months ago
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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,
I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs the bam file?
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator :
thank you!