svaba
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walaj
Structural variation and indel detection by local assembly
Hi there, Thanks for the great software! I have found that some entries in the output VCF have duplicate IDs. This is one example but it is happening in most...
Hello Jeremiah, I have an error while trying to run SvABA, similar to the one Tiffany had but that does not seem to be linked. I have run the following...
Sometimes, SvABA runs into infinite loops. When I rerun the job exactly as is, it goes through to completion just fine. Without actually knowing the code, I think it might...
Hi, I'm trying to extract all discordant reads while running svaba using the `--write-extracted-reads` option but it failed due to memory limit (30G). How big of memory would I need...
Hi, I have been testing out your new program which I was hoping would filling a niche in our tumor sv pipeline. After running svaba on a number of in-house...
Hi, I'm encountering the following error. Svaba runs as normal for a few minutes (judging from the logs), then I get the following error: > --- Loaded non-read data. Starting...
Thank you for all your hard work! I would like to understand the targeted detection (argument -k) a bit more. In the targeted mode, would rearrangements with one breakpoint in...
hi, in line 239 of svaba-annotate.R script: "## +- or -- msut be -- or ++. Starts on side where gstrand == rarstrand" the "## +- or --" part should...
Not an issue as such (apologies), but do you have any advice regarding possible merging of the sv.vcfs into a multi-sample file? bcftools norm/merge fails due to the ALT and...
Hi, Current svaba supports 10x genomics barcode "BX", while other protocol and aligner may name barcode other tag names like "CB". Can svaba add an option to regnozie the tag...
