Query regarding SV calls

[pwanj]

Hello,

I ran svaba on few BAM files (similar samples) . I observed that a SV call is made in some samples and not in others, even though the discordant reads can be seen in the BAM files for all samples in IGV. Is there any filtering criteria or cut-off used to decide when a SV call is made and written to the *sv.vcf files? (Mode: tumor only )

I would appreciate your help.

Thanks!

[pwanj]

Here in the above example, the SV call is made for the top sample, but not for the other 2 samples. However, the discordant reads are present in all 3 samples. Please can you tell me why?

I would appreciate it. Thanks!

[walaj]

Thanks for bumping this and for your patience. Can you check the *.bps.txt.gz file to see if the SV called in sample 1 is listed for the other two? *.bps.txt.gz has the most comprehensive record of detected SVs and there are filters of several types that are used to move it to the final VCF. If you could send to [email protected]. I'll keep the issue here open until we resolve, and can post the resolution here for others.