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ALT field only contains symbolic <INS>, <DEL>, ... tags instead of actual ALT nucleotide sequence #365

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JoannaTan opened this issue Jan 23, 2024 · 0 comments

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@JoannaTan
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Hi Tobias
In the issue #344 you mentioned that "for an insertion there should always be an ALT sequence".
I am using Delly version 1.1.6 (admitely old given the current version is 1.2.6 ... but it is an already containerized version I was given to use) and akin observation made in #344 by @ClarenceHsiang, the ALT column of Delly output VCF contains symbolic values

While given your comment ("...will try to fix this in the next version...") I suspect the version of Delly used by @ClarenceHsiang also had some shortcoming.
In which version of Delly are "insertion always the ALT sequence" ?
Thanks

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