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Published 20 hours ago • verified publisher icon gymreklab

statSTR handling of chrY

Open hopedisastro opened this issue 1 year ago • 1 comments

I get the following error when running statSTR on a VCF with chrY loci genotyped by ExpansionHunter:

File "/root/micromamba/lib/python3.10/site-packages/trtools/utils/utils.py", line 312, in GetHardyWeinbergBinomialTest if gt[1] not in allele_freqs.keys(): IndexError: tuple index out of range

I think this is because the 'GT' is not in the format of two numbers eg '0/1' or '1/1' but just one integer eg '0' or '1' to represent the hemizygous chrY.

hopedisastro avatar Jan 22 '24 23:01 hopedisastro

Just wanted to check on the above. Would the tools now support chrY positions?

Just noticed the following in the description, but would be great if does now support haploid calls:

TRTools only currently supports diploid genotypes. Haploid calls, such as those on male chrX or chrY, are not yet supported but should be coming soon.

br2890 avatar Mar 28 '24 11:03 br2890