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).
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/.
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