Hi @giuliag89
Great, thanks for sharing. The tool seems to be working correctly, and negative values are accepted.
Try removing the space between the - and 5.
So this: TERM > -5
instead of TERM > - 5
The two filters might need to be in separate filter blocks. I didn’t get any data passing through when combined on the same line. All filters in any single run are combined with a logical “AND” by default. Meaning, all need to be true for data to pass through. There is a toggle for an “OR” on the form too should you need that.
That should be enough so you can try different queries to see what filters for your purposes, without running into an error with the syntax adjusted a bit. I wasn’t sure if the compressed format was causing some random issue or not – but I didn’t find that to be actual (yea!). So using the current compressed format should be fine. I can see that you were testing that as well, or were converting to tabular format for another reason… You could output plain text VCF instead from BCFTools Call if you want to try using other tools to directly filter/query for any reason. BCFTools understands the compression, other tools may not.
Hope that helps!