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#SnIPRE PREP SCRIPTS

The objective of the two scripts (snipre_prep_bash.sh and snipre_prep.R) is to create an input file for SnIPRE program (http://med.stanford.edu/bustamantelab/software.html).

##snipre_prep_bash.sh

This script takes in as input all the .bam files used to create the .vcf file, a fasta file and a gff file. The output is a .coverage file with the following format...

Group:Pos Total_Depth Average_Depth Depth_one Depth_two Depth_three Depth_four Depth_five

Group1.1:2 2 0.20 0 1 0 0 1

The bash script creates a .coverage file using GATK command, and then splits up the .coverage file based on unique Group name.

Note : This bash script must be run prior to snipre_prep.R as its output files are used by the R script.

The .jar file needed for this bash script (GenomeAnalysisTK.jar) can be downloaded from https://www.broadinstitute.org/gatk/.

##snipre_prep.R

This R script takes in eight command-line arguments to create an output file that can be used by the SnIPRE program. The eight command-line arguments are (in order)...

1) .vcf file
2) starting bee column number (positive integer) of the vcf file (1-based indexing)
3) ending bee column number (positive integer) of the vcf file (1-based indexing)
4) SnpEff file (for Format Specifications, see Part 2)	
5) gff file (for Format Specifications, see Part 5)
6) Folder where output files from snipre_prep_bash.sh are located (path name)
7) nout : outgroup x 2 (positive integer)
8) npop : population size x 2 (positive integer)

The output file created from this R script has the following format...

Group PR FR PS FS tsil trepl nout npop XP_12345678.1 10 3 3 10 445 483 20 16 XP_12345678.2 3 10 10 3 544 834 20 16

Rscript		snipre_prep.R		sample.vcf	10	17	syn_nonsyn_sample.eff	sample.gff	/coverage/Groups		16	20