Retrieve single rows from large pileup file

cowman · 01-14-2011, 02:38 AM

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

dan · 01-16-2011, 02:40 PM

http://search.cpan.org/~lds/Bio-SamT...ge_information

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

Dan.

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01-14-2011, 02:38 AM	#1
cowman Member Location: North west UK Join Date: Jan 2011 Posts: 13	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

01-16-2011, 02:40 PM	#2
dan wiki wiki Location: Cambridge, England Join Date: Jul 2008 Posts: 266	http://search.cpan.org/~lds/Bio-SamT...ge_information ... should do the job... let me know! Dan. __________________ Homepage: Dan Bolser MetaBase the database of biological databases.