Joost Kranendonk

If wanted, I could add a test for this similar to [`test_annotation()`](https://github.com/neithere/argh/blob/master/test/test_assembling.py#L209).

Ah. [Not maintained](https://github.com/neithere/argh/issues/124#issuecomment-383645696). Got it!

@brainstorm you could try using GNU Parallel: ```sh parallel bgzip ::: *.vcf ``` This will multiple instances of `bgzip` each one with a different file. The number of parallel instances...

I am greatly sorry, I have missed your last comments in the end... POLA is a good thing! You're right, as it also implements switches `-d` and `-c`; similar in...

Here's another example: input ``` ST4.03ch10 28888 . ATG AC,ACA 326.806 . ...;AN=4;AO=9,6;CIGAR=1M1D1X,1M2X;DP=19;DPB=16;DPRA=0,0;EPP=5.18177,8.80089;EPPR=7.35324;GTI=1;LEN=2,2;... GT:DP:AD:RO:QR:AO:QA 0/1/1/2:19:2,9,6:2:79:9,6:369,242 ``` output ``` ST4.03ch10 28888 . AT A 326.806 . ...;AN=4;AO=9;CIGAR=1M1D1X;DP=19;DPB=16;DPRA=0;EPP=5.18177;EPPR=7.35324;GTI=1;LEN=1;... GT 0|1|1|0 ST4.03ch10 28889...

> DPRA=1.87482,1.8716 @ikkextoch thanks for your input. In your case, the `DPRA` doesn't seem to be affected, is it?

@ikkextoch, thanks. Pretty robust but not flexible workaround. I am using an infamous Perl oneliner with a simple regex substitution on the VCF output (in a pipe): ```sh perl -pe...

@tseemann Thanks for the suggestion! `bcftools annotate` is a very powerful tool, I use it very frequent. However, it is not able to solve this problem. One could remove the...

Hi everyone, any progress on this? We'd like to keep the conda-env location packed within the project directory to keep everything nice and together, rather than using the default environment...

I would like to raise interest for this issue again. Our FASTA files have been compressed in BGZF (bgzip) to reduce space and are indexed using `samtools faidx`. Quite a...