Aaron Quinlan
Aaron Quinlan
I just pushed a commit (`65e377d29c`) to enable this through the use of a `-delim` option. The default delimiter for `merge` is now a "," instead of a ";". This...
A de novo in PIGA was missed on the X in a male because GATK called mom and dad HOM_REF yet male proband as HOM_ALT (when really HEM_ALT). We should...
No, was missed by de_novo. I think we should try to just make `de_novo` run the logic in `x-linked-denovo` as it is just another chromosome on which to look for...
Thanks for the contribution! As I understand it, the goal is to count the entire size of the fragment - is that correct?
Interesting, I am not sure what would have caused that or what changed to correct it.
Thanks for bringing this up. For compatibility with existing pipelines, I think documenting this difference (both online and in the CLI) would be best.
This is a great idea. I will look into it.
Is the `-header` option not working for you? The example below is from the bedtools2 repository (please file issues there): ``` curl -s ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz | gzcat | head -20 >...
Ah, I see now that you are referring to the fact that some of the tools don't support this functionality. In bedtools2, we are slowly working through standardizing the API...
I see your point Shaun. The problem with this, however, is that such a change could impact many existing pipelines that are crafted around the assumption that headers will not...