Petr Danecek

You could call `samtools bedcov` directly from your package. That's what I'll have to end up doing in my pipeline I am afraid

Yes, that's what I am doing ``` samtools bedcov -c file1.cram file2.cram file3.cram | cut -f1-3,7- | gzip -c > bedcov.txt.gz ``` Don't know yet what is the proper way...

Both can be used. Single `.` for brevity or `.,.,.` to express ploidy.

Partially missing arrays are fully handled in htslib. They were added later, and at that point the java implementation made the pragmatic decision to treat partially missing arrays as fully...

> `END` and `SVLEN` represent the same information. The new VCFv4.5 definition reflects this with `END` officially deprecated and redefined as computed field based on what's in `SVLEN`. Think of...

@davmlaw Sure. But that's a commit, not a discussion. An important decision like this should be discussed publicly.

I was unable to reproduce the problem. What version of tabix and bgzip are you using? This is what I did: # cat | while read A B C D;...

We could in principle allow arbitrary delimiters. It would make sense to store this with the other information in the header of .tbi file, but that would break backward compatibility....

Thank you for the report, this is now fixed in https://github.com/samtools/bcftools/commit/57b90721e0abc45de861361f3f175ae0edd1e715, the command `bcftools mpileup` should now exit with a non-zero code. I believe the rest of bcftools is already...

The VCF is not formatted correctly, the GT tag is not present in the header and in the FORMAT column, it should look like this ``` ##FORMAT= #CHROM POS ID...