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How to interpret slash (/) and vertical pipe (|) in GATK's vcf output?
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13 months ago
rimgubaev • 120
Russia/Moscow/Skoltech

The GATK output vcf file contains genotypes in which alleles could be separated both by vertical bar ("|") and slash symbols ("/"). For example: 0/1, 0|1, 0/0, 1|1. I found the explanation at EBI portal. It is said that

The vertical pipe | indicates that the genotype is phased, and is used to indicate which chromosome the alleles are on. If this is a slash / rather than a vertical pipe, it means we don’t know which chromosome they are on.

Does this statement correct for GATK output?

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14 months ago
h.mon 25k
Brazil

Does this statement correct for GATK output?

The very page you linked says so. This is part of the VCF specifications, so all correctly formatted vcf files should abide to it:

  • /: genotype unphased
  • |: genotype phased
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