search

mhguo1 / TRAPD

Burden testing against public controls
MIT License
49 stars 31 forks source link

Genes on chrX (i.e. _AR_) have zero hom and het counts in step 2b) #12

Open dioncst opened 4 years ago

dioncst commented 4 years ago

Hi Guo,

Thank you for your wonderful software. I have a question regarding counting carriers in public control cohorts. In my results, some genes on X chromosome (i.e. AR) have zero hom and het counts. I have tried gnomad.exome.r.2.1.1 and exac.r1, which resulted the same. Its weird and I'm not sure what the problem is.

Here is my code
python ./TRAPD/code/count_controls.py -v /data/download/gnomAD/ExAC.r1.sites.vep.vcf.gz -s /data/project/NOA_WES/vcf/snpfile.txt -o controlcounts.txt --database "exac" --pass

Best.

mhguo1 commented 4 years ago

Hello, thank you for your interest in our software. We currently are not configured to test non-autosomal chromosomes, but this is an area of active development and we hope to include it in our next release.