Tobias Rausch

If there are only a few samples available it's usually best to call them jointly: `delly call -g -x -o delly.bcf sample1.bam sample2.bam sample3.bam` The filtering then depends on your...

I suppose the merged.bcf file contains SV calls on all chromosomes? I would guess the delly classify step crashed, do you have the log files?

The quality scoring is indeed a bit of an issue because the input trace qualities are not very useful. The assemble command simply scales a flat quality prior by the...

Can't you easily do this by simply using the length of the sequence to calculate the required right trimming size? E.g.: `tracy basecall -o out.fa -f fasta in.ab1` `tail -n...

For the consensus sub-command you can just specify the trimming length, i.e.: `tracy consensus --trimLeft1 50 --trimRight1 50 ...` Or do you want such an option for the FASTA output...

For `tracy assemble` it's a simple majority vote. If you have, for instance, 3 traces and 2 support a gap `-` and 1 a nucleotide then the gap `-` is...

Indeed, it's a 50:50 chance in theory but in order to make the algorithm deterministic the code currently favours nucleotides over gaps.

This warning usually points to a problem in the library prep.

This doesn't look like Delly BCF files so please post this in the bcftools repository. Thanks.

Yes, for the CNV module delly does not yet do the reference lookup. That's indeed something that should be fixed.