Running Ancestry Analysis on Samples with no Hets Found
angelussong opened this issue · comments
Hi @brentp!
I'm working on a project trying to run some ancestry analysis on single-cell RNAseq samples. I used monovar for the variant calling and then peddy for the ancestry calling. All my samples had no hets in them. When I ran peddy, I saw this error:
Traceback (most recent call last):
File "", line 1, in
File "/wynton/home/fhuanglab/hsong1/.conda/envs/py2/lib/python2.7/site-packages/peddy/peddy.py", line 866, in het_check
sites, min_depth=min_depth)
File "cyvcf2/cyvcf2.pyx", line 76, in cyvcf2.cyvcf2.par_het
File "cyvcf2/cyvcf2.pyx", line 743, in cyvcf2.cyvcf2.VCF._finish_het
IndexError: index 0 is out of bounds for axis 0 with size 0
I'm wondering now if I could only run the ancestry analysis on these samples without the sex calling. Is that possible?
Thanks very much!
yes, it's possible, but this doesn't appear to be failing on the sex check part.
ancestry uses PCA. a sample without hom-ref calls will cluster away from all other samples which have hom-ref, het and hom-alt, so this will not be useful.
I am trying to figure out a solution for this, but don't have one at this time.
Any updates on that? I am having the same issue.
@ruthbpaula your samples also have no hets? I don't think that peddy can work well in that case.