Closed adamnovak closed 3 months ago
OK, I talked to Rajeeva and he told me that Lancet makes several graphs per variant. I added code to find the most centered one for each variant, and now I can indeed see this variant. Here's that deletion being taken by just the tumor reads:
These are now probably usable examples.
This fixes #427 sort of by making a BED that explains what variant is supposed to be seen.
I ran it like this:
Then I could put
http://[::]:8000/index.bed
into my local tube map as the BED file and browse the data.But, I think the data provided is not exactly what I really want to look at. It looks liek the called tumor variants are not actually in the graphs. For example, at
chr1:38506973-38506974
I am suppsoed to see aTumor-specific CTGGAATCCAGCAGCCCAGACTTCCACATCATAATTTTCTGGGGCAATGGTTTTCAAACTTCACTGTACG -> C DEL variant
. But the graph doesn't show a large deletion. Instead, that deleted sequence occurs 1 base into the leftmost node here, and I can see the softclips in the aligned tumor reads at their left ends, where they would read over the deletion edge that isn't present. Here's a screenshot of the softclips, with the tumor reads in red:So I now have a way to generate and host tumor-normal Lancet examples, including examples for larger indels, but the graphs coming from Lancet don't really seem to be the right ones.