Aaron Quinlan comments

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                                            Aaron Quinlan

feature request: sample counts for genotype at position in database

Can you use num_het and num_hom_alt for this?

allow using canonical transcript instead of highest impact

Hmm, I am not sure using the canonical impact is the best approach in the context of rare disease. I would rather manually refute candidates than miss them because they...

coverageBed coverage/number of features discrepancy

Have you checked to see if, by any chance, some of your BAM alignments are spliced? This could lead to an artificial McLain of the coverage if you don't use...

Fisher reports wrong results on some edge cases (overflow?) - #2

@brentp and I had discussed some of the instability in `fisher` and are favoring deprecation. @brentp do you have any ideas/comments about this discussion above?

bamtobed issue

can use the logic in the PR to fix similar issue for bamtofastq.

Invalid -f Argument in windowBed

Sorry, the docs are wrong. The `-f` option is not currently available in the window tool. You can easily get the behavior you want be adding slop to your A...

Question: Can Load Function add VCF to existing database?

Currently, the answer is no. There is no mechanism to update databases. One alternative would be to use vcftools' vcf-merge operation to combine old and new VCFs and then load...

Question: Can Load Function add VCF to existing database?

@duartemolha yes, you are correct. it is certainly possible to update a database, but we have not yet implemented it, mainly because there are alternatives (above). Some complexities exist -...

add other summary cohorts

Is it a VCF with frequencies? I can't open the link

Controlling delimiter in -nms option of mergeBed

Good suggestion, I'll look into it.