Petr Danecek

This looks like a duplicate of #1933. The current code does not contain an error message "Could not parse the file2:", could you please check if you get an error...

http://samtools.github.io/bcftools/howtos/index.html http://samtools.github.io/bcftools/bcftools.html#view http://samtools.github.io/bcftools/bcftools.html#query http://samtools.github.io/bcftools/bcftools.html#expressions

What is the motivation for this feature request?

Sorry it took longer to take longer. I just tested with the latest version we get ``` $ bcftools norm -m+any rmme.vcf | grep -v ^# chr1 219783256 . AAC...

The thresholds are extremely unlikely to work as is for different datasets, that's certain. The example is intended as an illustration only.

This is currently not supported. I can imagine adding this to the `merge` command as you are suggesting. Or it could be added as a more general feature, for example...

As commented here https://github.com/samtools/hts-specs/issues/769#issuecomment-2247510552, I did not find any mention of deprecating the INFO/END tag. This should be revisited and discussed more, I find that to be a terrible idea.

Starting with the last question, homozygous alternate genotypes count as variants relative to the reference genome. Regarding the genotypes, it depends on the actual reads and base qualities, and BAQ...

Can you create a small test case? As the problem is stated, it does not give enough information. I just need to see a minimal VCF and the exact commands...

This is a very difficult question to answer, it really depends on the specifics of the data - site density, the number of heterozygous and homozygous genotypes, allele frequencies at...