@@ -36,10 +36,15 @@ MetaSNP is mainly implemented in C/C++ and needs to be compiled.
I. Setup
--------
a) Change the SAMTOOLS variable in the **SETUPFILE** to your path to Samtools.
a) Change the SAMTOOLS variable in the **SETUPFILE** to your path to samtools.
If you don't have samtools, you can find it [here](http://samtools.sourceforge.net/):
http://samtools.sourceforge.net/
a) Change the HTSLIB variable in the **SETUPFILE** to your path to htslib.
If you don't have htslib, check your samtools folder first or download it [here](http://www.htslib.org/):
http://www.htslib.org/
b) Change the BOOST variable in the **SETUPFILE** to your path to BOOST library.
If you don't have boost, you can find boost [here](http://www.boost.org/users/download/):
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@@ -76,8 +81,10 @@ Workflow:
## Required Files:
***'all\_samples'** = a list of all BAM files, one /path/2/sample.bam per line (avoid duplicates!)
***'ref_db'** = the reference database in fasta format (f.i. multi-sequence fasta)
***'gen\_pos'** = a list with start and end positions for each sequence (format: sequence_id start end)
***TODO! Format 'db\_ann'** = [optional] a gene annotation file for the reference in [general feature format](http://www.ensembl.org/info/website/upload/gff.html)(GFF).
***'gen\_pos'** = a list with start and end positions for each sequence in the reference (format: sequence_id start end)
## Optional Files:
***'db\_ann'** = a gene annotation file for the reference database.
