Extracting Modifier/gene from .vcf file

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18 months ago

Ihor • 0

Hello, I cannot figure out to which modifier/gene corresponds the last array of values(i.e GT:AD:AF....). Thanks! enter image description here

vcf gene VEP modifier • 733 views

ADD COMMENT • link updated 18 months ago by Pierre Lindenbaum 161k • written 18 months ago by Ihor • 0

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your question is not clear to me. What are those reds marks ? The variant is REF=T/ALT=G and the sample is heterozygous T/G.

ADD REPLY • link 18 months ago by Pierre Lindenbaum 161k

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Oh, just ignore the red marks(it is for my convenience). I need to extract "MODIFIER" from each record, but I do not know which one corresponds to VAF. I see that there are multiple "MODIFIER", "ENSG", "ENST", etc but which one is the right one? I got this VEP but do not fully understand why we have multiple "MODIFIER" for each CHROM POS(i.e 13813 in this case).

ADD REPLY • link 18 months ago by Ihor • 0

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I got this VEP but do not fully understand why we have multiple "MODIFIER"

https://en.wikipedia.org/wiki/Alternative_splicing

ADD REPLY • link 18 months ago by Pierre Lindenbaum 161k

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