Generic Interval file format

Coffer

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Jun 18, 2011, 10:13:33 PM6/18/11

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I would like to take information from an excel file for IBS or IBD
shared segments between individuals which has the following format:
[str:name][int:chromosome#][int:start][int:end]

The generic interval file format does not accept a basic
18294933 36839276 Lowell_Kauffman
18294933 70427442 Nikolas_Kauffman
24230230 52059138 Bonnie_Schrack
21208405 26206660 L_Kauffman
21208405 98251139 S_Kauffman

Coffer

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Jun 18, 2011, 10:16:05 PM6/18/11

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post continued. sigh

The generic interval file format does not accept a basic listing like
shown where I lose the chromosome number information.

How do I format a basic interval file, which will have up to several
thousand lines covering chromosomes 1-22 to get my segment intervals
into SAVANT and displayed?

Wayne

Andrew

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Jun 20, 2011, 4:59:49 PM6/20/11

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Hi Wayne,

Generic interval files require a chromosome for each line. If you are
missing chromosome number information for a line, the line must either
be removed or a dummy name must be used (ie. chr?).

Hope that helps,
Andrew

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