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Old 05-30-2012, 12:33 AM   #1
NestorNotabilis
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Default Low frequency indel detection

Hi,
Can anyone recommend software particularly suited for very low frequency indel detection as might be applied to ultra-deep targeted sequencing (UDT-seq) datasets where coverage exceeds 1000x? Choices seem limited. Am getting the impression scripting around samtools mpileup output might be the most robust strategy. Any thoughts anyone?

Many thanks.
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Old 05-31-2012, 11:04 AM   #2
Artem
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I am also interested in indel annotation, if you find any good solutions please post.
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Old 05-31-2012, 11:23 AM   #3
bioinfosm
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I agree .. you would need to parse the pileup file and then use your own thresholds. Perhaps use the simple common filters and start with that indel list.

For annotation, seattleSEQ (http://snp.gs.washington.edu/SeattleSeqAnnotation/) is an option and so is TREAT (shameless self plug - http://www.ncbi.nlm.nih.gov/pubmed/22088845)
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Old 05-31-2012, 11:25 AM   #4
bioinfosm
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Quote:
Originally Posted by NestorNotabilis View Post
Hi,
Can anyone recommend software particularly suited for very low frequency indel detection as might be applied to ultra-deep targeted sequencing (UDT-seq) datasets where coverage exceeds 1000x? Choices seem limited. Am getting the impression scripting around samtools mpileup output might be the most robust strategy. Any thoughts anyone?

Many thanks.
ohh well, here is another option, though am not sure if variants includes indels
http://seqanswers.com/forums/showthread.php?t=18541
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