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CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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Lofreq call-parallel applies filters with --no-default-filter option specified #127

Open gamabunta313 opened 2 years ago

gamabunta313 commented 2 years ago

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 commented 1 year ago

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 commented 1 year ago

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