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Clarify interpretation of slash (/) and vertical pipe (|) in GATK's vcf output?

This post has some explanation about the use of slash (/) and vertical pipe (|) in GATK's vcf output.

Apparently, a slash (/) indicates that "we don’t know which chromosome they (alleles) are on". If this is the case, why does my VCF have many (virtually all) slashed (/) allele calls for loci with a denoted chromosome and position?

For example,

CM014970.1 4450225 . C T 31.37 . <VARIOUS INFO> 0/0:2,0:2:6:0,6,49 0/0:2,0:2:6:0,6,49 ./.:0,0:0:.:0,0,0

are the called alleles on chromosome CM014970.1 or is it unknown?

vcf gatk formatting
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written by evoclive • evoclive

1 answer

If this is the case, why does my VCF have many (virtually all) slashed (/) allele calls for loci with a denoted chromosome and position?

if you're using short reads, one can only phase variants if two variants are found one the same reads. So finding phased variants is more difficult with short reads than with long reads.

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written by Pierre Lindenbaum Pierre Lindenbaum

I don't understand how that answers the point about not knowing "which chromosome they are on" when loci with slashes have stipulated chromosomal information, e.g.:

CM014970.1 4450225 . C T 31.37 . <VARIOUS INFO> 0/0:2,0:2:6:0,6,49 0/0:2,0:2:6:0,6,49 ./.:0,0:0:.:0,0,0

To clarify: are the called alleles on chromosome CM014970.1 or is it unknown?

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written by evoclive • evoclive

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