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Copy path015_swartssnps2.sh
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19 lines (8 loc) · 1.08 KB
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#!/bin/bash -l
module load gcc jdk/1.8 tassel/5.2.14 plink/1.90 vcftools/0.1.13
#fixing header
head -n 835 MinimallyFilteredWithNAM_InbredLandraces_InbredTeosintes.vcf > header.txt
cat header.txt MinimallyFilteredWithNAM_InbredLandraces_InbredTeosintes_agpv3_ConvertedTo_agpv2.vcf > MinimallyFilteredWithNAM_InbredLandraces_InbredTeosintes_agpv3_ConvertedTo_agpv2_newheader.vcf
run_pipeline.pl -Xmx15g -fork1 -vcf AOMexGBS2_ZeaGBSv27impV5.vcf -includeTaxaInFile AOMexGBS2_indFilt70.txt -fork2 -vcf MinimallyFilteredWithNAM_InbredLandraces_InbredTeosintes_agpv3_ConvertedTo_agpv2_newheader.vcf -includeTaxaInFile SwartsKeepTaxa_indFilt70.txt -combine3 -input1 -input2 -mergeGenotypeTables -fork4 -filterAlign -input3 -filterAlignMinCount 421 -export MergeSwartsAnna_80 -exportType Plink -runfork1 -runfork2 -runfork3 -runfork4
#421 is 80% of 526 samples. sites with 20% or less missing data
run_pipeline.pl -Xmx15g -fork1 -Plink -ped MergeSwartsAnna_80.plk.ped -map MergeSwartsAnna_80.plk.map -PrincipalComponentsPlugin -covariance true -endPlugin -export pca_MergeSwartsAnna_80.txt -runfork1