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Old 08-23-2010, 02:55 PM   #1
ragowthaman
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Location: Seattle, USA

Join Date: Nov 2009
Posts: 12
Default Pileup representation of indels

Hi All,
I trying to understand the pileup output (with -c option) in little more detail. Little more than what sourceforge says.

I have made three table with my understanding about regular pileup columns and at the line which talks about indels (3rd column with a '*'). Can anyone go thru my tables and say, if I misunderstood something. I warn new users, it is my understanding, and i am pretty sure, i am wrong at couple places. So, please DO NOT use this as your reference. Instead visit sourceforge page here.

Thanks very much in advance,
If you are running short of time, you can at least look at the columns highlighted in red.

Apologize for PDF file. It is is hard, I can work on other ways.

Thanks very much list,

Gowthaman
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File Type: pdf My_interpreation_of_pileup.pdf (183.2 KB, 33 views)
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Old 04-30-2011, 07:12 PM   #2
masterpiece
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Location: malaysia

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Posts: 40
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hi ragowthaman,

I may not be able to help you, but your info helped me a lot. I've looked everywhere about details on pileup but find none. Until i find this, really solve the mystery.

Thanks for sharing

kamal
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