ChrX variants are not been identified in reference panel fasta

[akhilpampana]

Hello,

I am trying to harmonize chromosome X variants to determine allele directionality for meta-analysis. I am having difficulty getting the harmonization done because its not matching with the reference file. I have tried multiple iterations and nothing worked. Can you be able to help me out with this?

Here is the code:

gwaslab --input AoU_NTproBNP_chrX_nonPAR_03242026.tsv --fix-chr --harmonize --ref-seq /home/apampana/.conda/envs/gwaslab/hg38.fa --out AoU_NTproBNP

Sample Input:

Although I have the file and I am not getting matched correctly - can you help me with this?

[Cloufield]

Hi,
thanks for the feedback. Indeed there is a bug for loading chrx from fa.
Just updated to v4.1.4 to fix this. Please try the new version.