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Old 11-19-2010, 10:47 AM   #2
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Location: california

Join Date: Aug 2009
Posts: 7
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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,
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