Commit 11a75552 authored by eboulanger's avatar eboulanger
Browse files

readme

parent 59a1f911
......@@ -10,8 +10,10 @@ You will need to install the following software:
- [VCFtools](https://vcftools.github.io)
- [BCFtools](https://samtools.github.io/bcftools/)
- [PLINK v1.9](https://www.cog-genomics.org/plink/1.9/)
- [PGDSpider](http://www.cmpg.unibe.ch/software/PGDSpider/)
You will need to have the following R packages:
adegenet, polysat, pegas, vcfR, hierfstat, coda, radiator, pcadapt
## 01-SNPfiltering
......@@ -171,9 +173,9 @@ Finally, the script converts the final adaptive and neutral .vcf files in .bed .
and .strct_in format necessary for downstream analyses.
The conversion to genepop format for use of GENODIVE (to calculate kinship) is done with
the PGDSpider GUI.
input: neutral.vcf and population map, output: neutral.gen.txt
outputted .gen.txt file: add information on first line (otherwise genodive won't recognise format)
the PGDSpider GUI.
input: neutral.vcf and population map, output: neutral.gen.txt
outputted .gen.txt file: add information on first line (otherwise genodive won't recognise format)
To run the script, set arguments:
$1 = input file (vcf)
......
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