Aaron Quinlan comments

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                                            Aaron Quinlan

Genotype filter using wildcard with gt_alt_freqs > 0.3

When you say it did not work, do you mean you know for certain there are such variants and none were returned?

Patch test.sh to verify process substitution support

Thanks for this! By the way, I will get to the other patches you provided after the 19th. I am buried in grants and other deadlines until then. Sorry for...

GroupBy: Settable parameter for suppressing re-ordering of columns

Hi Axel, Can you provide an example of your desired behavior?

Update merge.rst

Well, version sort is not available for the default versions of many OS. I would rather assume -V is not present, but we could always make a note about the...

unionbedg

Could you make sure that both files are sorted correctly? ``` sort -c -k1,1 -k2,2n N25sort.bedgraph sort -c -k1,1 -k2,2n T25sort.bedgraph ```

gene :: disease lookup.

Current plan is to use VEP "annotation dump" to support this.

the -is option for pairToPair documentation might not be up to date

Yes, thank you Ada.

release prep

I think it would be great to add support for de novos when reporting candidate CHs. The challenge is that one cannot be confident that it causes a true CH...

Sorted input has out of order record

Thanks for reporting this. It appears to be a logic bug, as changing the chromosomes in `test_a.bed` to "A" or "X" or "1" seems to work. @38 could you please...

bedToBam function problem!

It looks like your input files may not be 4 column (tab separated) BEDGRAPH filers as required. Have you checked that?