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GATB / DiscoSnp

DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.
https://gatb.inria.fr/software/discosnp/
GNU Affero General Public License v3.0
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Multiple reference alleles output #34

Closed githubgig closed 2 years ago

githubgig commented 2 years ago

Hello,

I'm running DiscoSNP with -c 3 --branching 0 --no_low_complexity with a reference genome. Many SNPs that map to genome are showing multiple reference alleles (see below example). I've used DiscoSNP before both with and without genome, but never faced this issue.

_Scaffold_1 ACGGCA Scaffold_1 AG Scaffold_1 AGA Scaffold1 AGAAAGGCGGAAAAACATTCGAAAGATAGTG

pierrepeterlongo commented 2 years ago

I do not understand the issue. Several variants map the same location of the same scaffold?

githubgig commented 2 years ago

Hi Pierre,

I just realized this was an issue with the inserts and deletions and not SNPs. Sorry for the bother.

githubgig commented 2 years ago

Closing the issue