Estimation of Recent Shared Ancestry Using ERSA
Hi there,
I am trying to estimate recent shared ancestry using ERSA2.1. However, when I run the below command, I get "no_sig_rel" for all individuals.
ersa --segment_files=mydata.match --control_files=ceu.match --output_file=mydata.out --confidence-level 0.8
From PiHAT calculations there does appear to be related individuals in the dataset, with PiHAT scores as high as 0.5.
As a sanity check I went on to run the example in the ERSA read me file (see command below).
ersa --segment_files=data/family.match --control_files=data/ceu.match --pair_file=data/pairs.txt --output_file=example.out --confidence-level 0.8
And I received the same "no_sig_rel" for all but 1 pair of individuals.
Has anyone else had experience running this program? Am I leaving something out in the command? Any help would be greatly appreciated.
Many thanks,
Caragh
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Would you be able to shared your syntax? I managed to get ersa1.0 working using their python scripts but the results are still giving me "no_sig_rel" for most of the individuals, despite their PiHAT stating otherwise.
I'll have a look at my code and share it later today. However I'm not 100% sure I used it correctly (in the fifth degree everyone turned out to be related which I'm very sure of is not the case). How many samples do you have?
I was using ersa for ~200 genomes. Essentially:
python ersa chr*.match(essentially ersa on all .match files generated)I'm currently not planning to try ersa further but would be happy to hear your feedback.