Hi there,
I used soap2 in order to align 45 Gig ilumina reads over an indexed reference. Now I should use soapsnp to get the consensus sequence and to call snp. The output of sopa2 should be sorted though! The problem is that if I have a 153 Gigb file (which represent only chromosome 1 !!). How can I sort such a huge file? I was trying the unix sort command, but will it use an amount of memory comparable to the size of the file to sort (I don't know whether I will be able to access a computer with such an amount of free memory)?
thanks for your help
I used soap2 in order to align 45 Gig ilumina reads over an indexed reference. Now I should use soapsnp to get the consensus sequence and to call snp. The output of sopa2 should be sorted though! The problem is that if I have a 153 Gigb file (which represent only chromosome 1 !!). How can I sort such a huge file? I was trying the unix sort command, but will it use an amount of memory comparable to the size of the file to sort (I don't know whether I will be able to access a computer with such an amount of free memory)?
thanks for your help
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