Hello! I've been running breakdancer on 1000genomes data and it works fine except it generates a LOT of inserts that I suspect are false positives. This makes finding real insertions difficult. Increasing the number of needed pairs for calling a variant to for example 4 diminishes the noise but doesn't remove it. Anyone else having this problem?
Another thing, when running breakdancer on many BAM-files at once it generates completely different data compared to running them individually. For I example I find the same deletion in every single one of 20 individuals but when combining them in the bam2cfg script this deletion disappears.
Thank you for your time!
/Magnus
Another thing, when running breakdancer on many BAM-files at once it generates completely different data compared to running them individually. For I example I find the same deletion in every single one of 20 individuals but when combining them in the bam2cfg script this deletion disappears.
Thank you for your time!
/Magnus
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