fgsv
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fulcrumgenomics
Tools to gather evidence for structural variation via breakpoint detection.
Enhancing the README to better communicate how this toolkit works and should be used.
It'd be helpful to be able to identify the position with the most support @clintval
See release 0.2.0. The issue is that the git commands use the last tag.
Looking at [what falls through as a possible deletion](https://github.com/fulcrumgenomics/fgsv/blob/70519fdce32324fc4b912cfc524aa00aed137282/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala#L222C14-L222C14), I think fgsv categorizes the following as a "possible deletion" when it's more likely a "intra-contig rearrangment": 1. The left and...
Requirements: * run `bwa mem`: * _without_ the -M option (-M marks shorter split hits as secondary). * use the `-Y` option (use soft clipping for supplementary alignments). Run: *...
fgsv generates an output BAM from the pileup phase that has tags like: ``` be:Z:0;left;from;read_pair be:Z:0;left;into;read_pair be:Z:0;left;from;split_read be:Z:0;left;into;split_read be:Z:0;right;from;split_read be:Z:0;right;into;split_read ``` where records from the same template (or same read...
I'm envisioning we could add parameters like: ``` --min-split-reads (default: 0) --min-read-pairs (default: 0) --min-total-support (default: 1) ``` The only problem with doing this is that we would no longer...
Currently `AggregateSvPileup` merges breakpoints that have left and right breakpoints within a distance threshold of each other, regardless of the type of read evidence of the breakpoints: split-read (breakpoint occurs...
I.e. https://github.com/fulcrumgenomics/fgsv/blob/main/docs/05_Tools.md
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Tools to gather evidence for structural variation via breakpoint detection.