get_seeds_inv4.sh

seeds_inv4.sh

#Run tassel from the get_list.R

module load gcc jdk/1.8 tassel/5

run_pipeline.pl -Xmx64g -fork1 -h All_SeeD_2.7_chr4_no_filter.unimputed.hmp.txt -export -exportType VCF -runfork1


sed '11q;d' All_SeeD_2.7_chr4_no_filter.unimputed.vcf > header.vcf

#This cuts lines BEFORE header
sed '1,10!d' All_SeeD_2.7_chr4_no_filter.unimputed.vcf > first.vcf

#This cuts lines below the header
sed -e '1,11d' All_SeeD_2.7_chr4_no_filter.unimputed.vcf > last.vcf

# transpose the header and awk and transpose again - give it the proper naming
cat header.vcf | tr '\t' '\n'| awk -F":" '{print $1}'| tr '\n' '\t' > middle.vcf

#Get the list of dups
cat middle.vcf | tr '\t' '\n' > testheader.vcf
uniq -d testheader.vcf > dups.txt

# Middle has no line ending so add one
sed -i -e '$a\' middle.vcf

# Put it all back together, this is our new vcf file
cat first.vcf middle.vcf last.vcf > seeds.vcf

# Get the range
~/bin/vcftools_0.1.12b/bin/vcftools --vcf seeds.vcf --from-bp 172000000 --to-bp 177000000 --chr 4 --recode --out range_chr4.vcf

# Now use the filter list from R and pass to vcftools and pull out the seeds stuff 

sed -e '/^M/d' temp_keep.txt > gone.txt

~/bin/vcftools_0.1.12b/bin/vcftools --vcf range_chr4.vcf.recode.vcf --keep gone.txt --recode --out inds_sites_filtered_chr4_inv.vcf

# Get rid of the duplicates defined above
~/bin/vcftools_0.1.12b/bin/vcftools --vcf inds_sites_filtered_chr4_inv.vcf.recode.vcf --remove dups.txt --recode --out inds_sites_nodups_chr4_inv.vcf

# Convert this to plink
~/bin/vcftools_0.1.12b/bin/vcftools --vcf inds_sites_nodups_chr4_inv.vcf.recode.vcf --plink --out inv4_plk

# Convert to plink binary, and exclude the SNPs that are not on any chromosome
module load plink/1.90
plink --file inv4_plk --make-bed --out inv4_bplk

# Get the indIDs from plink file to associate with the metadata and altitude
cut -f2 inv4_plk.ped > out.inds.txt

# Run flashpca - install in your path
flashpca --bfile inv4_bplk --stand center --numthreads 8 --outvec eigenevector_inv4 R --outload SNPload_inv4R --outval eigenvalue_inv4R

srun -p bigmemh --mem 36000 --pty bash