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dataPrep
Commits
11a75552
Commit
11a75552
authored
Mar 13, 2020
by
eboulanger
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readme
parent
59a1f911
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README.md
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@@ -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
...
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@@ -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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