#generate VCF for whole genome GWAS PCA samtools mpileup -ugf hormaphis_cornu_26Sep2017_PoQx8.fasta *.srt.rmPCRdup.bam | /Genomics/grid3/users/preilly/bin/bcftools/bin/bcftools call -m --threads=16 -Oz -o aphid.bothLibraries.raw.vcf.gz /Genomics/grid3/users/preilly/bin/bcftools/bin/bcftools filter -e "QUAL<20" -O z -o aphid.bothLibraries.filteredQUAL20.vcf.gz aphid.bothLibraries.raw.vcf.gz nohup /Genomics/grid3/users/preilly/bin/bcftools/bin/bcftools view -i 'F_MISSING<0.2' aphid.bothLibraries.filteredQUAL20.vcf.gz -Oz -o aphid.bothLibraries.filteredQUAL20_missingGeno0.2.vcf.gz & nohup /Genomics/grid3/users/preilly/bin/bcftools/bin/bcftools filter -i 'TYPE="snp"' aphid.bothLibraries.filteredQUAL20_missingGeno0.2.vcf.gz -Oz -o aphid.bothLibraries.filteredQUAL20_missingGeno0.2_SNPs.vcf.gz & nohup /Genomics/grid3/users/preilly/bin/bcftools/bin/bcftools view -q 0.05:minor aphid.bothLibraries.filteredQUAL20_missingGeno0.2_SNPs.vcf.gz -Oz -o aphid.bothLibraries.filteredQUAL20_missingGeno0.2_SNPs_MAF0.05.vcf.gz & module load vcftools/0.1.15 vcftools --gzvcf aphid.bothLibraries.filteredQUAL20_missingGeno0.2_SNPs_MAF0.05.vcf.gz --recode --recode-INFO-all --thin 1000 --out aphid.bothLibraries.filteredQUAL20_missingGeno0.2_SNPs_MAF0.05_thinned1000 #generate VCF for enrichment region PCA bcftools index catrim.Hcor_94ind_dp10.vcf.gz vcftools --remove-indv catrim.Hcor_HW04L01_Gr.targetreg_sorted_markdup \ --remove-indv catrim.Hcor_JRC13_Gr.targetreg_sorted_markdup \ --remove-indv catrim.Hcor_JRC17_Gr.targetreg_sorted_markdup \ --remove-indv catrim.Hcor_JRC20_Gr.targetreg_sorted_markdup \ --gzvcf catrim.Hcor_94ind_dp10.vcf.gz --recode \ --out catrim.Hcor_94ind_dp10_noLowInd bcftools view -i 'F_MISSING<0.2' catrim.Hcor_94ind_dp10_noLowInd.recode.vcf -Oz -o catrim.Hcor_94ind_dp10_noLowInd_missingGeno0.2.vcf.gz bcftools filter -i 'TYPE="snp"' catrim.Hcor_94ind_dp10_noLowInd_missingGeno0.2.vcf.gz -Oz -o catrim.Hcor_94ind_dp10_noLowInd_missingGeno0.2_SNPs.vcf.gz bcftools view -q 0.05:minor catrim.Hcor_94ind_dp10_noLowInd_missingGeno0.2_SNPs.vcf.gz -Ov -o catrim.Hcor_94ind_dp10_noLowInd_missingGeno0.2_MAF0.05_1mb.vcf