ekg
commented
3 years ago The linear gap model in edyeet is probably not suitable for this target. If you apply it as part of pggb, with smoothxg afterwards, it should be fine. But directly inducing the graph with seqwish is going to generate a mess if that's the only step.
I would suggest using wfmash. There you may find a need to increase the -l and -a parameters or turn of adaptive banding to get the best alignment.
On Fri, Oct 9, 2020, 21:57 Eugene Goltsman notifications@github.com wrote:
Hi Erik, I'm using edyeet to induce a graph (w seqwish) on a small set of sequences that contain mostly large indels (~4-6kb). It seems like in this case edyeet is trying too hard to do base-level alignment where it should've either terminated or opened a large gap. In the first case below, there is a 5 kb inverted duplication (I know it because it was synthetically introduced) at pos 7544324 on Accn1, but the aligner is attempting to extend the alignment past the breakpoint following the initial ~50kb match. Similarly, in the second case a 5kb inversion occurs at pos 7,573,027, but instead of terminating the alignment, edyeet is pushing through the area of virtually no identity. This leads to tiny graph segments and structures that later get called as bogus variants. I tried raising the -p cutoff to 95%, but that results in the entire 50kb block containing the inversion not being reported. It seems that this cutoff applies across the entire block. Is there anything else you could suggest tweaking that works at a local level, sort of like a gap extension vs mismatch penalty in smith-waterman ? Thanks!
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egoltsman
Hi Erik, I'm using edyeet to induce a graph (w seqwish) on a small set of sequences that contain mostly large indels (~4-6kb). It seems like in this case edyeet is trying too hard to do base-level alignment where it should've either terminated or opened a large gap. In the first case below, there is a 5 kb inverted duplication (I know it because it was synthetically introduced) at pos 7544324 on Accn1, but the aligner is attempting to extend the alignment past the breakpoint following the initial ~50kb match. Similarly, in the second case a 5kb inversion occurs at pos 7,573,027, but instead of terminating the alignment, edyeet is pushing through the area of virtually no identity. This leads to tiny graph segments and structures that later get called as bogus variants. I tried raising the -p cutoff to 95%, but that results in the entire 50kb block containing the inversion not being reported. It seems that this cutoff applies across the entire block. Is there anything else you could suggest tweaking that works at a local level, sort of like a gap extension vs mismatch penalty in smith-waterman ? Thanks!