Lofreq call-parallel applies filters with --no-default-filter option specified

[gamabunta313]

I am working with Lofreq2.1.2. I run the following command to call only indels:
bin/lofreq call-parallel --pp-threads $threads $input -f ${reference} -o ${filename}_indel.vcf -Q 20 -B -m 17 -a 0.01 --only-indels --no-default-filter --call-indels

From intermediate files I observed that indel are called, however, even if I specified "--no-default-filter" option, lofreq applies lofreq filter. The result is the loss of all the indels called since all have QUAL lower the default --snvqual-thresh. It is fundamental to me leaving all the raw indel calls since I am working on realign reads to call indel.
I thank you in advance for your willingness.

[GaloGS]

Hi, I am having the same issues also when using lofreq call. I observed that basically lofreq does not use the arguments I provide. It does not use --no-default-filter and it does not use --force-overwrite, so processes always throw the error "Cowardly refusing to overwrite exsiting file".

[Mailinnia]

I'm experiencing the same issue with lofreq v. 2.1.5