svaba
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walaj
Structural variation and indel detection by local assembly
I've just run `SvABA` on a small region of chr X, but the results are quite difficult to interpret just from the VCF files. I tried looking at the `*.alignments.txt.gz`...
I tried annotating VCF obtained from SvABA using AnnotSV. The SV TYPE column was replaced with ALT column.
Hi Jeremiah, I've ran SvABA on some test BAMs and benchmarked it against other modern SV callers - it performs well, having the highest F-score on NA12878 germline sample. Unfortunately,...
Hi, I'm wondering if svaba is expected to have deterministic output, or if it's possible to get deterministic output? I've run svaba with the same settings on the same tumor-normal...
Hi @walaj , I successfully ran svaba and annotated the output with your instructions. Just a quick question, is svaba detect only intrachromosomal translocations? In all my samples I just...
Hello, I was wondering what the correct way to calculate the VAF is? I tried AD/DP but a lot of the regions have a value greater than 1 and they...
Hi, We have been running multiple SV callers on high coverage data (275x tumor / 156x normal). We have observed that SvABA seems to be making quite a few SV...
Hi, I've noticed that the paths to the bam files I'm using in my svaba runs are used as the sample IDs in the vcf files. I'm wondering if this...
Hi Jeremiah, I've been seeing a few examples of somatic SVs where AD>0 and DP=0. I saw from issue [#29](https://github.com/walaj/svaba/issues/29) that AD can be greater than DP since discordant reads...