[Awesome]

Hi Mansequencer,

For some reason, MSORT doesn't work with files over a certain size. It works just fine for small files using the command:

$ msort -k 8,n9 mapped.out > mapped.out.sort

To get around this, you can use the SORT command that is native to most Linux and Unix distributions:

sort -t $'\t' -k 8f,8 -k 9n,9 mapped.out > mapped.out.sort

To check to see if your files are indeed sorted, you can always isolate just the two columns in question, the chromosome and position:

cut -f 8,9 mapped.out.sort > col_89.txt

SOAPSNP generates a huge file on purpose. Either of the other formats GLFv2 and GPFv2 may give a smaller footprint output. Try those.

Best of luck,
-Awesome