Petr Danecek

From various reasons the `-t/-T` option works differently in `mpileup / call`. I hope if you just pipe through `bcftools view -t`, it works?

There is the `bcftools norm --rm-dup` option, would that be a good solution to your problem?

Hi, this requires a small test case to reproduce the problem, the screenshots do not provide enough information to understand and debug the problem.

I doubt this is a bug in bcftools. Is it possible that the numbers reflect different number of header lines, rather than different number of data lines? Try `bcftools view...

The program usage pages explains how it arrives to its results ``` Determine sample sex by checking genotype likelihoods (GL,PL) or genotypes (GT) in the non-PAR region of chrX. The...

The outputs you showing are lengthy and not informative to debug the problem. Any chance you could make the VCFs available? small test case would be sufficient.

Can you please show the exact command and the version of bcftools you are running? If not latest, can you please upgrade and check if the problem persist? If yes,...

1.9 is quite old. Can you please try with the latest version? http://samtools.github.io/bcftools/howtos/install.html Even then, I am afraid that without a full reproducible test case there is not much I...

It would be interesting to see what the missed SNV looked like. It would be helpful to see an IGV screenshot and the raw mpileup output for that site.

This would require also the BAM and the reference for testing. Showing just the result again is not helpful.