Debug

Common issues

• If you get the error:

could not load: libhts.so

Try: export LD_LIBRARY_PATH=./htslib/

• Empty -bounds.txt/-genotype.txt:

Check the mapping quality (MAPQ) of your reads. STRling requires a default minimum MAPQ of 40 for non-repetitive reads. If the MAPQs are low, and you’d still like to consider these reads, you can change the MAPQ setting using: -q, –min-mapq=MIN_MAPQ Ensure to do this at all workflow stages where it is an option.