Problem with long deletion about svaba

[walaj]

H Victor, Are you looking as well in the *.sv.vcf file? SvABA puts longer events into this file.

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On Jul 17, 2017, at 6:07 AM, Victor Wang ***@***.***> wrote: Hi Walaj, I tried to use SvABA on long deletion range from 1mbp to 150mbp in simulated bam file. SvABA works well when only small indel are included. However, when I start to include those long deletion into the bam SvABA failed to detect anything, not even the small indels. I checked the contig bam file, and those contigs do include correct breaking points. BTW, default germline settings were used for the analysis. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[VicBioDev]

*sv.vcf and *unfiltered.sv.vcf both contain header info only, no event detail. Simulated bams were generated by VarSim 0.7.9.
Here is a link to the vcf files and log for both scenarios.

[walaj]

Thanks for the data Victor, that's really helpful. I'll take a look this weekend and get back to you.

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On Mon, Jul 17, 2017 at 9:24 PM, Victor Wang ***@***.***> wrote: *sv.vcf and *unfiltered.sv.vcf both contain header info only, no event detail. Simulated bams were generated by VarSim 0.7.9. Here is the link <https://1drv.ms/f/s!ApgA2CjIgb7Gp_wus0iQl2KfRHaecQ> to the vcf files and log for both scenarios. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#10 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGmfiD_m70jSdq1I4eS4wpsyuFwj-ar3ks5sPAkygaJpZM4OZxT4> .

[walaj]

I'm not able to unzip the files after I download them, something strange with how OneDrive is serving them perhaps? Is there another way you could serve them?

[VicBioDev]

Sorry for the wait. I moved the files to Google Drive. Let me know if you have problem accessing them.

[walaj]

Hi Victor,
I'm not sure what is the issue just by looking at the VCFs and log files. They seem to have been run very similarly. Would you at all be able to share a portion of the simulated BAMs so I can just recreate the issue and let you know? Thanks for your patience with this.