Petr Danecek

I am reluctant to add checks like that, certain awareness is required from users when working with command line tools. Few notes if such check should be added: - this...

How would it work if the genotype was, say, triploid or tetraploid, and there were multiple indels of different length? I am struggling to define the behavior for a generalized...

I am unable to comment without seeing the data, ideally a small bam slice + corresponding fasta reference chunk. EDIT: This script can be used to create a small test...

If you think it is a bug, please provide a small test case which makes you believe that. Otherwise I'd look for errors in the logic of the boolean expression...

Is there any chance you could provide a small test case? I am unable to comment without seeing the data unfortunately.

> Unfortunately I can not share the exact sequences. I may be able to generate an artificial dataset with similar characteristics for testing purposes. @fd-bnt Could you perhaps create an...

> I tried the experimental –indels-2.0 but unfortunately it did not finish after 6h I just pushed a commit that will likely fix the issue of `--indels-2.0` never finishing.

> ``` > # on seq4d > cd /local/scratch01/jkb > bcftools mpileup -B -L 99999 -d 999999 --fasta-ref /nfs/srpipe_references/references/SARS-CoV-2/MN908947.3/all/fasta/MN908947.3.fa -Q 1 -a AD 3000.sam 2>/dev/null |bcftools call -vm - 2>/dev/null|grep...

What I found thus far: 1) The `--indels-2.0` calls the indel variant okay, so likely there is a good chance it will help, @fd-bnt. 2) Regarding the difference between https://github.com/samtools/bcftools/commit/b5cbcd5d047a8478ac892d8fec4a5c4ffc4e0a48...

I'd suggest to use https://github.com/pd3/mpileup-tests/blob/main/misc/create-bam-test. It creates a slice of the bam file and the reference genome, so the new coordinates are completely nonsensical. It also renames the sample and...