Petr Danecek

It should use index and jump to the correct location. Not a top priority at the moment, but it's good to have this issue open when someone gets bored later.

The FORMAT=DP/AD/ADF/ADR tags are supposed to be high-quality bases, as described in the header. Your question suggests that you are observing something else. In such case we'll need mode details...

I don't see a problem, the normalization is doing the right thing: ``` 1234567 ACGCTCCTCCTCCAGA ref ACGCTCC---TCCAGA ori ACG---CTCCTCCAGA norm ``` In the original form the variant is `7:CTCC>C` which...

This should normally work. Is it possible that you are looking at sites that were not generated by `mpileup` and were instead inserted by the `call -i` option from the...

Not ``, but maybe `*`.

I think @mp15 meant to use `*` ALT allele which is a valid way how to specify missing alleles due to conflicting variants. A valid VCF notation then would be:...

In the point 1, I don't understand the proposal to disallow multiple ALT alleles in gVCF fields and this would not be a good thing. In the point 3, he...

The error messages actually do indicate the problem: the "Parent=transcript:" keyword is not found in some records, see an example of a supported file format here: ftp://ftp.ensembl.org/pub/grch37/release-84/gff3/homo_sapiens/Homo_sapiens.GRCh37.82.gff3.gz Maybe there could...

That would be great, thanks

The documentation excerpt pasted above states that gene, transcript and CDS lines are required, but in your example the transcript is not shown. (By the way, the program must have...