Null outputs from Sliding_Window() about staarpipeline-tutorial HOT 2 CLOSED

Hi @pelinunal,

Thank you for your question. This is technically not an error, but rather indicates that your sliding windows do not have a sufficient number of variants to form a valid variant set so that the results will be NULL. With a quick look, could I ask if your data come from a Whole-Genome Sequencing (WGS) study containing variants from both coding and noncoding regions? Your sample size (11,021) is large, but the number of variants (1.3 million) for this chromosome is relatively small under the sample size being considered, which resulted in NULL results.

Best,
Xihao

from staarpipeline-tutorial.

Dear @xihaoli,

Indeed, the number of the variants is small in the chr. This is the result of filtering the INFO score >0.9 as a post-QC step after the imputation of the WGS data. Thank you for the enlightment on the problem. I will try with less strict INFO score filtering.

Bests,
Pelin

from staarpipeline-tutorial.