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Old 03-12-2016, 02:40 PM   #1
PandoraMid
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Default CNV and Ion Torrent

Hi! I work with Ion Torrent for detect some mutations in 2 specific genes: BRCA1 and BRCA2 (so I sequence just these regions), but the problem of this sequencer/software is that there's no way to detect some macro-deletion or macro-rearrangement in general (or if there's I don't know).

My question is: there's some software that start with a BAM file (or other output from Ion) and can detect this macro-rearrangement?

Thank you
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Old 03-14-2016, 02:29 AM   #2
tristan dubos
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Hi , i m working in BRCA 1 and 2 too !! What do you mean about macro-rearrangement ? Big INDEL ?
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Old 03-14-2016, 05:09 AM   #3
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Yes, in particular macro-deletion!
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Old 03-14-2016, 05:12 AM   #4
tristan dubos
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Witch variant caller do you use ? And witch part of BRCA are you exterminating (only Exon) ?
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Old 03-14-2016, 08:42 AM   #5
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Exon and junction Introd and exon
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Old 03-15-2016, 12:09 AM   #6
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An what is your pipeline actually ? do you find SNP and INDEL ?
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Old 03-16-2016, 11:02 AM   #7
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The software already reads snp and small indel, my problem is with exon's deletion. So i ask if one of you use a particular software for detect this "deletion of one or more exon" just in this two genes. I sequence just exon and junction intron-exon of this two genes.
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Old 03-17-2016, 12:18 AM   #8
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I understood your point. I didn't use a particular software for that because like you we looked only after SNP and small INDEL only for the moment. But we can detect deletion of exon if we looked in the depth coverage in the data control part when we check the run of sequencing.
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