Description
Hello,
I have just started to use AlphaFamImpute and am running a dataset with about 80 founders, 160 F1's and 1300 F2's. I am starting with just one chromosome with 486252 markers to troubleshoot and get things going. I currently don't have all my read depths calculated, so I am using just genotypes.
The way my data is setup is that I have high confidence in the founders genotypes, the F1 had medium depth sequencing and were imputed from their direct parents and the F2's have low pass sequencing and were imputed from the panel of all haplotypes. I am looking to either clean up the imputed genotypes or possilbly do some re-imputation.
My first test I had a pedigree file, a genotypes file and a map file. The output was:
My command:
AlphaFamImpute -out testAFI -ped trios.goodongenonly.txt -genotypes chr10withnames.012 -map chr10.012.pos
Reading in AlphaGenes format: chr10withnames.012
Now imputing chromosome 10 using markers 0 to 486252
Imputing family of F04F684_tame and F05F469_aggr, using 1 high-density offspring.
/usr/local/lib/python3.12/site-packages/alphafamimpute/tinyhouse/ProbMath.py:83: RuntimeWarning: divide by zero encountered in log
vals = np.log(vals)
Segmentation fault (core dumped)
Any helps or hints to get this working?