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<dup-10> in one of the alternate alleles #342

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ghost opened this issue Sep 1, 2021 · 2 comments
Open

<dup-10> in one of the alternate alleles #342

ghost opened this issue Sep 1, 2021 · 2 comments

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@ghost
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ghost commented Sep 1, 2021

Hi,
One of my variants called has a <dup-10> in the middle of the alternate allele. Pretty sure no vcf tool out there can process what this means. Can you advise what this is? See the variant below:

chr11   1017406 .       T       TTGGTGAAGGGTGTGGGTAGCCTGCTGCTGGTGGCCGACGTGGTGTGGGCC<dup-10>GGTGTGGGCCACAGGGGTTCTGGTGCCTGTACTGGTGTGGTTGGGGGTGA   172     PASS

B
@aryarm
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aryarm commented Mar 2, 2022 •
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Just chiming in to say that we've also encountered this problem. It would be great if this could be corrected within the var2vcf_valid.pl script.

@aryarm aryarm mentioned this issue Mar 2, 2022
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@greenbagels
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greenbagels commented Jul 19, 2023 •
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Hi, I just encountered this issue when trying to normalize VarDict's output using bcftools; has anyone figured out what the alternate allele is?

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@greenbagels @aryarm