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ANGSD / angsd

Program for analysing NGS data.
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hwe_pval unknown #440

Open aguilar-gomez opened 2 years ago

aguilar-gomez commented 2 years ago

I am using angsd version 0.935-53-gf475f10. I had the following error: -hwe_pval is unknown will exit

I found this SNP filter on the wiki but I am not sure why it is not working. Here is my full command:

angsd -bam $bamlist -out $outname -minInd 200 -setMinDepthInd 1 -minMapQ 25 -minQ 25 -remove_bads 1 -uniqueOnly 1 -only_proper_pairs 1 -GL 1 -doMaf 1 -doMajorMinor 4 -doGlf 2 -SNP_pval 1e-6 -nThreads 10 -ref $REF -minMaf 0.05 -setMaxDepthInd 50 -doCounts 1 -skipTriallelic 1 -sites $sites -rf $regions -hwe_pval 1e-4 -sb_pval 1e-4 -edge_pval 1e-4

Thank you, Diana

murielgb commented 2 years ago

I am not sure but maybe try with using -dosnpstat 1. From my understanding, this is what calculated the hwe pval so if you want to filter on this, you need first to calculate.

Muriel

ANGSD commented 2 years ago

Dear all, yes, you need to set dosnpstat 1 and set -doHWE 1, I can see this is unclear, I am keeping this issue open so I dont forget about it.