adding files for Molecular Ecology group interested in host anemone GWAS

pinskylab · Apr 1, 2021 · fd7910f · fd7910f
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commit fd7910f
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Showing 22 changed files with 18,998 additions and 2,544 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
 /.ipynb_checkpoints
 /data/FIL_6.recode.vcf
 *.vcf
+*APCL_HostAnemAssoc*
diff --git a/notebooks/.ipynb_checkpoints/MolEcoClass_GWAS_dataprep-checkpoint.ipynb b/notebooks/.ipynb_checkpoints/MolEcoClass_GWAS_dataprep-checkpoint.ipynb
diff --git a/notebooks/MolEcoClass_GWAS_dataprep.ipynb b/notebooks/MolEcoClass_GWAS_dataprep.ipynb
diff --git a/script_output/ForMolEcoGroup.chrom-map.txt b/script_output/ForMolEcoGroup.chrom-map.txt
diff --git a/script_output/ForMolEcoGroup.log b/script_output/ForMolEcoGroup.log
@@ -3,14 +3,15 @@ VCFtools - 0.1.15
 (C) Adam Auton and Anthony Marcketta 2009
 
 Parameters as interpreted:
-	--vcf data/FIL_6.recode.vcf
-	--keep script_output/ForMolEcoGroupAnemSppLigIDs.txt
-	--recode-INFO-all
+	--vcf script_output/SnpsWithContigIDsForMolEcoGroup.vcf
+	--chrom-map script_output/ForMolEcoGroup.chrom-map.txt
 	--out script_output/ForMolEcoGroup
-	--recode
+	--plink
 
-Keeping individuals in 'keep' list
-After filtering, kept 1521 out of 2908 Individuals
-Outputting VCF file...
+After filtering, kept 1521 out of 1521 Individuals
+Writing PLINK PED and MAP files ... 
+	Read 485 chromosome mapping file entries.
+	PLINK: Only outputting biallelic loci.
+Done.
 After filtering, kept 1005 out of a possible 1005 Sites
-Run Time = 6.00 seconds
+Run Time = 1.00 seconds
diff --git a/script_output/ForMolEcoGroup.maf0.2gen0.1NoRelatedness.bed b/script_output/ForMolEcoGroup.maf0.2gen0.1NoRelatedness.bed