Updated the documentation.

Author: StuntsPT

TestData/README.md

@@ -1,51 +1,52 @@
-#Test Data for  *Structure_threader*
+# Test Data for  *Structure_threader*
 
 In this directory you will find the data that was used to benchmark *Structure_threader*.
 
-##Contents (in alphabetical order):
+## Contents (in alphabetical order):
 
-* Chr1.str.tar.xz
-* Chr22.str.tar.xz
-* benchmark.sh
+* BigTestData.str.tar.xz
 * extraparams
 * joblist.txt
 * mainparams
 * TestData.structure
 
-###Chr1.str.tar.xz
+### BigTestData.str.tar.xz
 
-This file is a fastStructure formatted input file which was used to benchmark fastStructure. This is a **huge** SNP file (16854 SNPs) which was obtained from the [1000 genomes project](http://www.1000genomes.org). The file was downloaded from [here](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz), and was then filtered using vcftools with the following criteria:
+This file is a fastStructure formatted input file which was used to benchmark fastStructure. This is a large SNP file (604 SNPs) which was obtained from the [1000 genomes project](http://www.1000genomes.org). The file was downloaded from [chromossome 22](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz), and was then filtered using vcftools with the following criteria:
 
 * only biallelic, non-singleton SNV sites
 * SNvs must be at lest 2KB apart from each other
 * minor allele frequency < 0.05
 
 The used command was:
 
-./vcftools --gzvcf
-ALL.chr1.phase3_shapeit2_mvncall_integrated_v4.20130502.genotypes.vcf.gz
---maf 0.05 --thin 2000 --min-alleles 2 --max-alleles 2 --non-ref-ac 2 --recode --chr 1 --out Chr1
+    ./vcftools --gzvcf \
+    ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz \
+    --maf 0.05 --thin 2000 --min-alleles 2 --max-alleles 2 --non-ref-ac 2 \
+    --recode --chr 1 --out Chr1
 
 This was the criteria that was used on the *admixture* [analysis of the 1000 genomes project](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/admixture_files/README.admixture_20141217).
 
-The file was then converted to structure format with [PGDSpider](http://www.cmpg.unibe.ch/software/PGDSpider/), and compressed with xz.
+The file was then converted to structure format with [PGDSpider](http://www.cmpg.unibe.ch/software/PGDSpider/).
+To further reduce the dataset (for faster benchmarking), the file was then processed with `cut` and `head` and finally compressed with xz.
 
-###Chr22.str.tar.xz
+The used commands were:
 
-This file is similar to the one above, but it is from [chromossome 22](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz) instead of chromossome 1. As such it contains fewer SNPs (2719).
+    cut -d " " -f 1-604 BigData.str > BigData604SNPs.str
+    head -n 1002 BigData604SNPs.str > BigTestData.str
+    tar cvfJ BigTestData.str.tar.xz BigTestData.str
 
-The file processing was done in the same way as for Chr1.
 
-###extraparams and mainparams
+### extraparams and mainparams
 
 The STRUCTURE paramater files that were used in the benchmarking process.
 
-###joblist.txt
+### joblist.txt
 
 The joblist used to benchmark *ParallelStructure*. Consists of 16 jobs, 4 values of "K" with 4 replicates each.
 
-###TestData.structure
+### TestData.structure
 
 This is the datafile itself  that was used in the benchmarking process.
 It contains 83 individuals, divided in 17 populations, represented for 29 SNP loci.
-There is aproximately 13% missing data in the file.
+There is approximately 13% missing data in the file.