Petr Danecek
Petr Danecek
What version of bcftools are you using? If it's the latest, any chance you could provide a test file for debugging?
New version 1.17 was just released. Can you please try with that? If the problem persists, we'd need to reproduce the problem locally with your BAM to explain what is...
I believe the edited BAM_CREF_SKIP checking code https://github.com/samtools/bcftools/blob/ef8b974dee6d3bc9f56e39a75997a64a13cbcaa1/bam2bcf_indel.c#L855-L859 simply skips these reads from realignment. I am imagining a proper fix would be to split the reads into parts and deal...
True, the option `--indels-2.0` is far from finished, but it is not intended for deprecation. I'll use the opportunity to document its current state and explain its main idea: it...
I am happy for the wording to be changed
Hi, this may be a bit late, but I just added an experimental (and for now hidden) option `bcftool view --hts-verbose`. Can you try it out please? If it works,...
Uh, there was a silly bug. Can you try now please? https://github.com/samtools/bcftools/commit/65cbaea1b7205bed87bf863ee7982a4df683f718
OK. I added the `-v, --verbosity` option to all commands and plugins. Hopefully this will be useful.
It would be better to attach a small test case (that is, VCFs) instead of screenshots as this does not allow us to run tests and debug the problem properly....
That's correct, `bcftools mpileup` skips secondary alignments by default. This can be controlled with the option ``` --skip-any-set STR|INT Skip reads with any of the bits set [UNMAP,SECONDARY,QCFAIL,DUP] ```