Question about strand information in Minda VCF Output

[YX-Yuan]

Hi,

I am currently using the merged VCF file generated by Minda for chromothripsis prediction with ShatterSeek and Starfish. However, I noticed that the strand information is not included in the INFO column of the VCF file, nor in the support.txt file. All BND events are recorded in the ALT field using the N]chr*:****] notation.

Could you please advise on how to correctly interpret the strand information from the Minda output? Additionally, would it be possible to include strand annotations in the INFO field in future versions, similar to the format used by Severus?

Thank you very much for your help and for providing such useful tools.

Best regards,
YX

[asherbryant]

Hello YX,

Thank you for the feedback.

We wanted Minda to be compatible with as many callers' VCF files as possible. All VCF files have ALT field notation for BNDs, but only a few record stand information. Adding strand information to Minda VCFs could possibly be added, but I believe there would always be ambiguity around INV strand if the original VCF files do not indicate this.

Best,
Asher

[amcpherson]

The ALT field notation for BNDs should include strand information for all callers, otherwise the caller is not outputting VCF according to the specification. Minda should also follow the spec and parse and output BND strand information correctly. Does minda not account for strand information for BND type SVs? If not, this makes the tool significantly less useful.