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Old 01-14-2011, 02:38 AM   #1
cowman
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Default Retrieve single rows from large pileup file

I want to retrieve about 20million specific rows from a pileup file with about 2billion rows. I can see the index command which I assume makes this possible but I cannot see the command to retrieve a specific row by chromosome and position. I want to extract the coverage from these rows.

I am expecting to embed this command in a perl script and call the command for each row I need, but if I can do in all at once that would be great.

Thanks for any pointers
Harry
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Old 01-16-2011, 02:40 PM   #2
dan
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http://search.cpan.org/~lds/Bio-SamT...ge_information

... should do the job... let me know!

Dan.
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