Why gatk VariantAnnotator required bam and coverage files
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Entering edit mode
7 weeks ago
QX ▴ 20

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,

gatk VariantAnnotator • 492 views
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Entering edit mode
7 weeks ago

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 ?

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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?

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1
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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
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thank you!

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