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[Bioc-devel] Include indel counts in applyPileups
6 messages · Martin Morgan, Julian Gehring, Michael Lawrence +1 more
On 02/13/2014 08:09 AM, Sean Davis wrote:
Hi, Martin. How difficult would it be to include insertions/deletions in seq and qual in the applyPileups method for PileupFiles? The use case is to look at the context around variants for increases mismatch rates. Indels will have a small impact on such calculations, but for completeness it would be nice to have.
Actually we're in the process of revisiting how pileups are calculated, so it's a great time to express what you'd like. Are you asking for per-position information on indel occurrence? Martin
Thanks, Sean [[alternative HTML version deleted]]
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Hi Sean, You can have a look at the 'bam2R' function from the 'deepSNV' package. This will extract the base/insertion/deletion counts, base call qualities, and other metrics strand-specific from a BAM file. Best wishes Julian
On 13/02/14 17:09, Sean Davis wrote:
Hi, Martin. How difficult would it be to include insertions/deletions in seq and qual in the applyPileups method for PileupFiles? The use case is to look at the context around variants for increases mismatch rates. Indels will have a small impact on such calculations, but for completeness it would be nice to have. Thanks, Sean [[alternative HTML version deleted]]
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