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2018-07-17 11:02:15 -0600 asked a question CNV breakpoints in read pile-up

Hi, I have a very rare example of a sub-exonic duplication, confirmed in the clinic. A different IGV-like tool enable the detection of break-points by showing miss-aligned read tails spanning the break-point. On the other hand, GB does not enable this break-point detection as the reads seem to be clipped off at the break-point and onward (where the sequence is miss-aligned). I've tried playing with the filters but it doesn't seem to help. The other break-point same story. Is there a way to enable GB visualise the miss-aligned read tails for break-point detection? *I wanted to upload and share the snippet but need 10 points to upload pictures (?)

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2017-05-16 07:56:40 -0600 asked a question Tandem duplications in Illumina's paired end data

Hi, I have 2 files on display at a single exon (paired-end pile-ups). One sample has a dup (probably tandem) while the other is control. I cannot recognize any difference in stacking patterns or read orientations. Are there any clues in the pile-up view that may indicate a presence of a short tandem dup (besides comparing depth)? Thanks!