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Help reading output (Genotype given in bp difference from reference) #60

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sngo318 opened this issue Feb 26, 2019 · 2 comments
Closed

Help reading output (Genotype given in bp difference from reference) #60

sngo318 opened this issue Feb 26, 2019 · 2 comments

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@sngo318
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sngo318 commented Feb 26, 2019 •
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chr:1 14070 . cctccctccctc . . . END=14081;RU=cctc;REF=3 GT:DP:GB:CI:RC:Q:INS 0/0:79:3,3:3-3,3-3:63,13,0,3:4.89157:344.217,96.4342

I was wondering why in the output the GB (Genotype given in bp difference from reference) is not a multiple of the motif length. For example, the motif cctc is 4 bp and the reference copy number is 3. Shouldn’t the genotype for a sample be a multiple of 4, whereas in this case the GB is 3 bp?

Any help would be appreciated.

Thank you
@nmmsv
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nmmsv commented Mar 2, 2019

Hello,
I think this relates to an older version of GangSTR, that had an error in the VCF fields.
The GB field that you see is actually number of copies of each allele.
We have a newer release (2.3) available, that should fix this issue.
Sorry for confusion.
Nima

@sngo318
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sngo318 commented Mar 7, 2019

Thank you

@nmmsv nmmsv closed this as completed Mar 7, 2019
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@nmmsv @sngo318