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ANGSD / angsd

Program for analysing NGS data.
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Association -doAsso 6 output files #430

Open clydeandforth opened 2 years ago

clydeandforth commented 2 years ago

Hi,

Could you explain more about the files produced as output of the Association dosage test with doAsso 6. There are two files produced alongside the .arg and .mafs.gz files. THese are labelled lrt.0.gz and lrt.1.gz.

I can see on the Angsd Wiki an explanation of an lrt file - however what is the difference between the two files? Does one of the files contain adjusted P values?

I ran the program like this (v0.935):

angsd -doAsso 6 -yQuant health.txt -Pvalue 1 -cov full_pca_15.cov -nThreads 6 -fai ref.fai -doMaf 4 -beagle beagle_file.gz

The output files look like this (lrt0):

zcat angsdput.lrt0.gz | head -n 2 Chromosome Position Major Minor Frequency N P beta SE high_WT/HE/HO Contig0 50 A G 0.087116 485 3.1103e-01 -3.033323 1.962232 344/51/1

and (lrt1): zcat angsdput.lrt1.gz | head -n 2 Chromosome Position Major Minor Frequency N P beta SE high_WT/HE/HO Contig0 50 A G 0.087116 485 1.8374e-01 -3.033323 1.962232 344/51/1

Thanks,

James

aalbrechtsen commented 2 years ago

I think you might have 2 phenotypes. Does your health.txt have two columns? angsd can run multiple phenotypes at the same time and will print out one "lrt" file per phenotype. If you only have 1 column in you phenotype file then it will only output 1 lrt file

-Anders