View source for Misc example

<pre>
Information on this page is deprecated and should be removed DRAGON.
</pre>
=Run Examples=
==Using glfv3==
<code lang="sh">
../dirty -samglf ceu.glf.list  -outfiles test.glf -doMaf 2 -fai numSort.Fai  -nLines 50000  -chunkSize 500 -nThreads 16 
</code>

==Using mpileup==
<code lang="sh">
./dirty.g++ -chunkSize 200000 -outfiles ASDF -doMaf 2 -nThreads 10 mpileup -g  -r 21:1-20000000 -I  ~/sample/*.chr21 >bcfoutput
</code>

First is programname.
Followed by the arguments used for dirty
Followed by mpileup and the arguments that will be bassed directly to SAMtools

From version 0.25, we can now get the nucleotide count for every site, for every sample. This is done by omitting the -g parameter

==Using tglf files==
cd into the teststuff subfolder

<code lang="sh">
../dirty.g++ -nThreads 1 -tglf lct.list -posfile lct.pos -nLines 100000 -outfiles GG -doMaf 15 -SNP_pval 1
</code>

If we want to estimate the SFS

<code lang="sh">
../dirty.g++ -nThreads 5 -tglf lct.list -posfile lct.pos -nLines 100000 -outfiles KK -realSFS 1
</code>

==Using soapfiles==
<code lang="sh">
../dirty.g++ -soap tsk.sub10.list -doMaf 2 -outfiles NEW10 -chunkSize 1000 -nLines 10000 -nThreads 4
</code>

-soap is filelist containing the soapfiles, each soapfile must be sorted according the chromosomename (lexical ordering), and position.


==Using simulated files==
These are .glf.gz files generated from simnextgen in misc subfolder, NB REMEMBER TO SUPPLY -nInd argument since these can't be inferred from the binary file.
<code lang="sh">
./dirty.g++ -sim1 misc/small.glf.gz -nInd 15 -outfiles results -doMaf 2
</code>