I am trying to index .bed like files from Leafcutter output as described here: Leafcutter sQTL
Leafcutter generates an .sh script to do this for each output file in
perind.counts.gz_prepare.sh which looks like this:
bgzip -f test_perind.counts.gz.qqnorm_chr1A \
tabix -p bed test_perind.counts.gz.qqnorm_chr1A.gz
The error I am getting is the following:
[E::hts_idx_push] Region 536959441..536959528 cannot be stored in a tbi index. Try using a csi index with min_shift = 14, n_lvls >= 6
tbx_index_build failed: test_perind.counts.gz.qqnorm_chr1A.gz
I am not sure how to deal with this error, and I need .tbi files to use as input for fastQTL. I have tried to use the
-m, --min-shift INT flag which works but generates .csi files which don't work with fastQTL.
Any help would be great thanks!