Question: Estimation of Recent Shared Ancestry Using ERSA
0
gravatar for Caragh
2.7 years ago by
Caragh 40
Ireland
Caragh 40 wrote:

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

ADD COMMENTlink written 2.7 years ago by Caragh 40

ersa2.0 worked for me (well, a bit), but it seems to have different synthax...

ADD REPLYlink written 2.7 years ago by WouterDeCoster39k

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.

ADD REPLYlink written 2.6 years ago by Caragh 40

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?

ADD REPLYlink written 2.6 years ago by WouterDeCoster39k

I was using ersa for ~200 genomes. Essentially:

  1. I removed all variants which weren't sequenced for all individuals and also excluded all indels (those gave some problems...). I had to split my variant file per chromosome because I had some problems in phasing "across" chromosomes. Major headache to find out what was going on.
  2. I converted my variants to plink format
  3. Using germline and beagle I performed phasing with the bash script "phasing pipeline" which can be found here: http://www.cs.columbia.edu/~gusev/germline/
  4. I ran 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.

ADD REPLYlink written 2.6 years ago by WouterDeCoster39k
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