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<INS> sequence missing in ALT field and represented as C<INS>, T<INS>, A<INS>, G<INS> #501
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Hi @leone93 I'm looking into this issue - is it possible for you to share a couple of occurences from the generated VCF? This would help a lot in identifying whats going on. As for the quantity of inserts, this is most likely a consequence of the newer version of sniffles also doing alignments, and possible separating calls that are sufficiently different. This is controlled by the merge param This is a new feature - did you check the variants to see if those get reported wrongly? Setting the mentioned parameter to 0 should emulate the 2.2 behaviour (i.e., no alignment checks being done on variants). Thanks, |
Hi @hermannromanek and @fritzsedlazeck ! For the multisample, I understand the --combine-pctseq paramter (it's the same of truvari), and maybe I will down it to 0.60 for my dataset. |
As the title says. Running sniffles 2.4 with this setting on my sample:
produces files with this value in the ALT field of many INS. Moreover, this error is propagated to to the multisample files created with:
More details. It does not depend on SVLEN (it is random from that point of view).
This error is not present on sniffles 2.2 (same settings), although I have some INS also there. Also, the quantity of INS in the multisample files is way lower in sniffles 2.2 compare to 2.4 on the same dataset (20 entries vs. 420).
Is there a way to have the proper sequence on the alt field for INS?
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