linsson

Hi and thank you very much fro your reply. I am using the same annotation (potato Itag) as agrigo2 and I downloaded the associations from agrigo2 site itself. In my...

I just noticed the difference in study (58 vs 263) and population (1185 vs 2392) GO terms. It's not completely clear to me why removing "--no_propagate_counts" should give that. Is...

Thank you very much. Of course, please keep data confidential. uhmm, it looks like I do not have permission to upload on that volume... If you give me an email...

Files sent. Could you download data?

Thank you very much for your answer. Unfortunately I am receiving the following error Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘seqSetFilter’...

I had to use a sort of workaround: ` #SNPRelate GDS input_VCF_name = opt$input_VCF input_GDS_name = sub(".vcf", ".gds", basename(input_VCF_name)) if (!file.exists(input_GDS_name)) { snpgdsVCF2GDS(input_VCF_name, input_GDS_name, method="copy.num.of.ref", ignore.chr.prefix="SL4.0ch") } input_GDS

I can't use just SeqArray GDS. This is what I get: >` gds=seqOpen("G2PSOLMerge.final.keep.recode.renamed.keep15161acc.recode.MinMeanDP15.MaxMiss0.95.recode.seqArray.gds") ` residualSNPset=snpgdsLDpruning(gds, ld.threshold=0.1 ) SNV pruning based on LD: Excluding 173,502 SNVs on non-autosomes Calculating allele counts/frequencies...