The function of "filter_cis" doesn't work in trans-eQTL analysis

[xwBio]

The function of "filter_cis" doesn't work in trans-eQTL analysis

[francois-a]

Hi, could you please provide the code you used to run tensorQTL? These SNPs are only filtered automatically in command-line mode. If you use tensorQTL as a module, you need to run the filtering step with filter_cis explicitly.

[xwBio]

Hi, many thanks for your reply.
Please find the below code I used for analysis:
python -m tensorqtl ${plink_prefix_path} ${wd}/${prefix}_rpkm.qnorm.std.bed.gz ${prefix}
--covariates ${wd}/${prefix}_combine_covariates.txt
--mode trans
--output_text
--return_r2
-o ${wd}

[francois-a]

Ok, so this should definitely work. What format are the variant IDs in your VCF in? filter_cis currently assumes that variants are in the format chr_pos_ref_alt_build, and extracts the variant position from these IDs.

[xwBio]

Ok, so this should definitely work. What format are the variant IDs in your VCF in? filter_cis currently assumes that variants are in the format chr_pos_ref_alt_build, and extracts the variant position from these IDs.

Thank you very much.
The SNP name in my genotype file was the rs number. That may be the reason for the issue.
If the tensorQTL could be applied to variants with the rs number for trans-QTL analysis, it would be much better.
Thanks for your great work again.

[francois-a]

This is fixed in the latest version. Thanks for catching this issue!