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brentp / peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF
MIT License
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Running Ancestry Analysis on Samples with no Hets Found #69

Open angelussong opened 4 years ago

angelussong commented 4 years ago

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!

brentp commented 4 years ago

yes, it's possible, but this doesn't appear to be failing on the sex check part.

brentp commented 4 years ago

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.

ruthbpaula commented 6 months ago

Any updates on that? I am having the same issue.

brentp commented 6 months ago

@ruthbpaula your samples also have no hets? I don't think that peddy can work well in that case.