Alistair Ward

Optional log file

8

Would it be possible to (optionally) output all log information to a defined file? We currently catch everything going to stderr and process to identify potential errors in our pipeline....

Subset should modify multiallelic sites

1

When subsetting a vcf file, it would be useful to trim all alleles from a multiallelic site that are not present in the samples being subsetted on. For example, consider...

Whitespace in INFO field

4

When running exomiser, I am receiving the error that the vcf file is malformed because the INFO field has whitespace in it. The vcf spec (4.4) explicitly states that whitespace...

Collapse introns

1

I wonder if it is worth removing / minimizing introns in the gene models, especially when looking at exome data? Take a gene like RAI1: The overwhelming majority of the...

Exon colouring on low coverage

1

Sometimes the exon is coloured purple, sometimes not.

Sometimes the exon is coloured purple, sometimes not.

Remove BRCA1 as startup gene

1

Since BRCA1 is a gene with known pathogenic mutations that often have to be reported, it is not good that we start in it! Starting in any gene also causes...

Integrate denovo-db

2

I think it would be interesting to also show known de novo variants in a gene (http://denovo-db.gs.washington.edu/denovo-db/).

Tooltip for variants table is in fixed location

5

If you scroll down, the tooltip still always appears above the table, so can be invisible if you scroll far enough, or just chopped off.

We could look at how to make it clear when a gene is on X, or Y, since this is an important distinction from the autosome. Also, maybe we should...