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05-30-2012, 01:33 AM
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#1 |
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Member
Location: Cardiff Join Date: Dec 2011
Posts: 19
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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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05-31-2012, 12:04 PM
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#2 |
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Junior Member
Location: Vancouver, BC Join Date: May 2012
Posts: 6
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I am also interested in indel annotation, if you find any good solutions please post.
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05-31-2012, 12:23 PM
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#3 |
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Senior Member
Location: USA Join Date: Jan 2008
Posts: 482
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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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05-31-2012, 12:25 PM
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#4 | |
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Senior Member
Location: USA Join Date: Jan 2008
Posts: 482
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Quote:
http://seqanswers.com/forums/showthread.php?t=18541 |
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