heterozygous structural variants
Is there any one knows that it is possible to get heterzygous SVs from the output of breakdancer, pindel etc? Or are the output from the 2 softwares all homozyous?
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Moved to a more appropriate forum. -
Breakdancer reports all variants for which it has enough support, in terms of then number of discordant read pairs, and does not call the genotype. Therefore, I think the output probably consists of both homo- and hetero-zygous variants.
You might want to look into the new GASVPro, which tries to call the genotype of variants based on depth of coverage around the breakpoints:
Sindi, S. S., Onal, S., Peng, L., Wu, H.-T., & Raphael, B. J. (2012). An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biology, 13(3), R22. doi:10.1186/gb-2012-13-3-r22Comment
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