Tags to snp

Question

[jaafari.omid]

Hi All Dears. This is Omid. I am using Tassel 3 (and 5). Now I am in the step entitled "TagsToSNPByAlignmentPlugin (the Discovery SNP Caller)" Unfortunately I faced with the error which says

"java.lang.IllegalArgumentException: TasselPipeline: parseArgs: Unknown parameter: -TagsToSNPByAlignmentPlugin".

I would be grateful if you could help me about this problem. Here is the command which I am using:

module load tassel3
run_pipeline.pl -Xms512m -Xmx10g -fork1 -TagsToSNPByAlignmentPlugin -i /home/omid/Tassel/tbt/GFO-1TBT.h5 -m /home/omid/Tassel/TOPM/GFO-1.topm -mUpd /home/omid/Tassel/TOPM/GFO-1WithVariants.topm -o /home/omid/Tassel/hapmap/GFO-1_chr+.hmp.txt -mnF 0.8 -mnMAF 0.02 -mnMAC 100000 -ref /home/omid/Tassel/ref/ref5.fasta -sC 1 -eC 50 -endPlugin -runfork1

Sincerely.

[WouterDeCoster]

Does this help?
- https://groups.google.com/forum/#!topic/tassel/Zbhcw5xANYM
- https://groups.google.com/forum/#!topic/tassel/n48pA13Dw3g

[jaafari.omid]

Many thanks. But I am using the tassel 3, and the plugin name is -TagsToSNPByAlignmentPlugin for tassel3, So why it gives me that error?

[WouterDeCoster]

Could you just check if DiscoverySNPCallerPlugin works? I have no experience with tassel at all, it's just the first thing that pops up when I google this.

[jaafari.omid]

Yes, Actually I just now did it and that error was solved but another error appeared about -mUpd option. I guess if I wan to use -DiscoverySNPCallerPlugin, my command should completely change. Thanks for your helps.

[WouterDeCoster]

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