B Bash Scripts

B.1 batch.sh

Script:

# /data/cjgwx7/tml_gpsm/scripts/bash/batch.sh

### Create fixed-width BLUPF90 genotype file for each subgroup
awk -F ' ' '{printf "%-15s%-50000s\n",$1,$2}' ../../raw_data/level2/c.txt > ../../raw_data/level2/c.txt_fw
awk -F ' ' '{printf "%-15s%-50000s\n",$1,$2}' ../../raw_data/level2/d.txt > ../../raw_data/level2/d.txt_fw
awk -F ' ' '{printf "%-15s%-50000s\n",$1,$2}' ../../raw_data/level2/l.txt > ../../raw_data/level2/l.txt_fw
awk -F ' ' '{printf "%-15s%-50000s\n",$1,$2}' ../../raw_data/level2/y.txt > ../../raw_data/level2/y.txt_fw
awk -F ' ' '{printf "%-15s%-50000s\n",$1,$2}' ../../raw_data/level2/cd.txt > ../../raw_data/level2/cd.txt_fw
awk -F ' ' '{printf "%-15s%-50000s\n",$1,$2}' ../../raw_data/level2/cl.txt > ../../raw_data/level2/cl.txt_fw
awk -F ' ' '{printf "%-15s%-50000s\n",$1,$2}' ../../raw_data/level2/cy.txt > ../../raw_data/level2/cy.txt_fw
awk -F ' ' '{printf "%-15s%-50000s\n",$1,$2}' ../../raw_data/level2/dl.txt > ../../raw_data/level2/dl.txt_fw
awk -F ' ' '{printf "%-15s%-50000s\n",$1,$2}' ../../raw_data/level2/dy.txt > ../../raw_data/level2/dy.txt_fw
awk -F ' ' '{printf "%-15s%-50000s\n",$1,$2}' ../../raw_data/level2/ly.txt > ../../raw_data/level2/ly.txt_fw
awk -F ' ' '{printf "%-15s%-50000s\n",$1,$2}' ../../raw_data/level2/dly.txt > ../../raw_data/level2/dly.txt_fw
awk -F ' ' '{printf "%-15s%-50000s\n",$1,$2}' ../../raw_data/level2/cdly.txt > ../../raw_data/level2/cdly.txt_fw

### Delete old .txt files
rm ../../raw_data/level2/*.txt

### Split files into batches of < 25,000 observations each
### Subgroup 1
cp ../../raw_data/level2/c.txt_fw ../../raw_data/level3/c/c.aa

### Subgroup 2
cp ../../raw_data/level2/d.txt_fw ../../raw_data/level3/d/d.aa

### Subgroup 3
cp ../../raw_data/level2/l.txt_fw ../../raw_data/level3/l/l.aa

### Subgroup 4
cp ../../raw_data/level2/y.txt_fw ../../raw_data/level3/y/y.aa

### Subgroup 5
split --verbose ../../raw_data/level2/cd.txt_fw -l12667 cd.
mv cd* ../../raw_data/level3/cd/

### Subgroup 6
split --verbose ../../raw_data/level2/cl.txt_fw -l13937 cl.
mv cl* ../../raw_data/level3/cl/

### Subgroup 7
split --verbose ../../raw_data/level2/cy.txt_fw -l13450 cy.
mv cy* ../../raw_data/level3/cy/

### Subgroup 8
split --verbose ../../raw_data/level2/dl.txt_fw -l18072 dl.
mv dl* ../../raw_data/level3/dl/

### Subgroup 9
split --verbose ../../raw_data/level2/dy.txt_fw -l17585 dy.
mv dy* ../../raw_data/level3/dy/

### Subgroup 10
split --verbose ../../raw_data/level2/ly.txt_fw -l18855 ly.
mv ly* ../../raw_data/level3/ly/

### Subgroup 11
split --verbose ../../raw_data/level2/dly.txt_fw -l18171 dly.
mv dly* ../../raw_data/level3/dly/

### Subgroup 12
split --verbose ../../raw_data/level2/cdly.txt_fw -l21015 cdly.
mv cdly* ../../raw_data/level3/cdly/

Log:

creating file `cd.aa'
creating file `cd.ab'
creating file `cl.aa'
creating file `cl.ab'
creating file `cy.aa'
creating file `cy.ab'
creating file `dl.aa'
creating file `dl.ab'
creating file `dy.aa'
creating file `dy.ab'
creating file `ly.aa'
creating file `ly.ab'
creating file `dly.aa'
creating file `dly.ab'
creating file `dly.ac'
creating file `cdly.aa'
creating file `cdly.ab'
creating file `cdly.ac'

B.2 renum.sh

Script:

# /data/cjgwx7/tml_gpsm/scripts/bash/renum.sh

### Copy necessary files into current directory
cp ../../intmd/pedigree_map/{ped_plus_intmd.txt,ped_intmd.txt,map_intmd.txt} .

### Copy genotype file into current directory
cp ../../raw_data/level3/c/c.aa .

### Run renumF90
renumf90 ../blupf90/renum.c_aa

### Save PLINK PED and MAP files
preGSf90 renf90.par

### Move important files to new location
mv renf90.dat toPlink.map toPlink.ped renadd01.ped c.aa_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/c/

### Remove unnecessary files
rm c.aa renf90.tables renf90.fields renf90.par

### Repeat above for each subgroup/batch combination

### Subgroup 2
cp ../../raw_data/level3/d/d.aa .
renumf90 ../blupf90/renum.d_aa
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped d.aa_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/d/
rm d.aa renf90.tables renf90.fields renf90.par

### Subgroup 3
cp ../../raw_data/level3/l/l.aa .
renumf90 ../blupf90/renum.l_aa
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped l.aa_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/l/
rm l.aa renf90.tables renf90.fields renf90.par

### Subgroup 4
cp ../../raw_data/level3/y/y.aa .
renumf90 ../blupf90/renum.y_aa
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped y.aa_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/y/
rm y.aa renf90.tables renf90.fields renf90.par

### Subgroup 5
cp ../../raw_data/level3/cd/cd.aa .
renumf90 ../blupf90/renum.cd_aa
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped cd.aa_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/cd/aa/
rm cd.aa renf90.tables renf90.fields renf90.par

cp ../../raw_data/level3/cd/cd.ab .
renumf90 ../blupf90/renum.cd_ab
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped cd.ab_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/cd/ab/
rm cd.ab renf90.tables renf90.fields renf90.par

### Subgroup 6
cp ../../raw_data/level3/cl/cl.aa .
renumf90 ../blupf90/renum.cl_aa
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped cl.aa_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/cl/aa/
rm cl.aa renf90.tables renf90.fields renf90.par

cp ../../raw_data/level3/cl/cl.ab .
renumf90 ../blupf90/renum.cl_ab
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped cl.ab_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/cl/ab/
rm cl.ab renf90.tables renf90.fields renf90.par

### Subgroup 7
cp ../../raw_data/level3/cy/cy.aa .
renumf90 ../blupf90/renum.cy_aa
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped cy.aa_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/cy/aa/
rm cy.aa renf90.tables renf90.fields renf90.par

cp ../../raw_data/level3/cy/cy.ab .
renumf90 ../blupf90/renum.cy_ab
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped cy.ab_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/cy/ab/
rm cy.ab renf90.tables renf90.fields renf90.par

### Subgroup 8
cp ../../raw_data/level3/dl/dl.aa .
renumf90 ../blupf90/renum.dl_aa
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped dl.aa_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/dl/aa/
rm dl.aa renf90.tables renf90.fields renf90.par

cp ../../raw_data/level3/dl/dl.ab .
renumf90 ../blupf90/renum.dl_ab
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped dl.ab_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/dl/ab/
rm dl.ab renf90.tables renf90.fields renf90.par

### Subgroup 9
cp ../../raw_data/level3/dy/dy.aa .
renumf90 ../blupf90/renum.dy_aa
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped dy.aa_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/dy/aa/
rm dy.aa renf90.tables renf90.fields renf90.par

cp ../../raw_data/level3/dy/dy.ab .
renumf90 ../blupf90/renum.dy_ab
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped dy.ab_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/dy/ab/
rm dy.ab renf90.tables renf90.fields renf90.par

### Subgroup 10
cp ../../raw_data/level3/ly/ly.aa .
renumf90 ../blupf90/renum.ly_aa
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped ly.aa_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/ly/aa/
rm ly.aa renf90.tables renf90.fields renf90.par

cp ../../raw_data/level3/ly/ly.ab .
renumf90 ../blupf90/renum.ly_ab
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped ly.ab_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/ly/ab/
rm ly.ab renf90.tables renf90.fields renf90.par

### Subgroup 11
cp ../../raw_data/level3/dly/dly.aa .
renumf90 ../blupf90/renum.dly_aa
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped dly.aa_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/dly/aa/
rm dly.aa renf90.tables renf90.fields renf90.par

cp ../../raw_data/level3/dly/dly.ab .
renumf90 ../blupf90/renum.dly_ab
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped dly.ab_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/dly/ab/
rm dly.ab renf90.tables renf90.fields renf90.par

cp ../../raw_data/level3/dly/dly.ac .
renumf90 ../blupf90/renum.dly_ac
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped dly.ac_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/dly/ac/
rm dly.ac renf90.tables renf90.fields renf90.par

### Subgroup 12
cp ../../raw_data/level3/cdly/cdly.aa .
renumf90 ../blupf90/renum.cdly_aa
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped cdly.aa_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/cdly/aa/
rm cdly.aa renf90.tables renf90.fields renf90.par

cp ../../raw_data/level3/cdly/cdly.ab .
renumf90 ../blupf90/renum.cdly_ab
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped cdly.ab_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/cdly/ab/
rm cdly.ab renf90.tables renf90.fields renf90.par

cp ../../raw_data/level3/cdly/cdly.ac .
renumf90 ../blupf90/renum.cdly_ac
preGSf90 renf90.par
mv renf90.dat toPlink.map toPlink.ped renadd01.ped cdly.ac_XrefID sum2pq freqdata.count Gen_call_rate ../../raw_data/level4/cdly/ac/
rm cdly.ac renf90.tables renf90.fields renf90.par

### Remove unnecessary files
rm ped_plus_intmd.txt ped_intmd.txt map_intmd.txt

B.3 ProcessPlinkF90.sh

Script:

# /data/cjgwx7/tml_gpsm/scripts/bash/ProcessPlinkF90.sh

### Subgroup 1
### Remove extra blank column
cut -d ' ' -f 1-6,8- ../../raw_data/level4/c/toPlink.ped > ../../raw_data/level4/c/toPlink_v2.ped

### Extract genotypes
cut -d ' ' -f 7- ../../raw_data/level4/c/toPlink_v2.ped > ../../raw_data/level4/c/toPlink_geno.ped

### Replace renumbered IDs with actual IDs
Rscript ../r/ProcessPlinkF90/c_aa.R

### Column bind columns 1-6 and the genotypes
paste -d ' ' ../../raw_data/level4/c/c_aa.fam ../../raw_data/level4/c/toPlink_geno.ped > ../../raw_data/level6/c.ped

### Subgroup 2
cut -d ' ' -f 1-6,8- ../../raw_data/level4/d/toPlink.ped > ../../raw_data/level4/d/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/d/toPlink_v2.ped > ../../raw_data/level4/d/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/d_aa.R

paste -d ' ' ../../raw_data/level4/d/d_aa.fam ../../raw_data/level4/d/toPlink_geno.ped > ../../raw_data/level6/d.ped

### Subgroup 3
cut -d ' ' -f 1-6,8- ../../raw_data/level4/l/toPlink.ped > ../../raw_data/level4/l/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/l/toPlink_v2.ped > ../../raw_data/level4/l/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/l_aa.R

paste -d ' ' ../../raw_data/level4/l/l_aa.fam ../../raw_data/level4/l/toPlink_geno.ped > ../../raw_data/level6/l.ped

### Subgroup 4
cut -d ' ' -f 1-6,8- ../../raw_data/level4/y/toPlink.ped > ../../raw_data/level4/y/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/y/toPlink_v2.ped > ../../raw_data/level4/y/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/y_aa.R

paste -d ' ' ../../raw_data/level4/y/y_aa.fam ../../raw_data/level4/y/toPlink_geno.ped > ../../raw_data/level6/y.ped

### Subgroup 5
### Batch 1
cut -d ' ' -f 1-6,8- ../../raw_data/level4/cd/aa/toPlink.ped > ../../raw_data/level4/cd/aa/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/cd/aa/toPlink_v2.ped > ../../raw_data/level4/cd/aa/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/cd_aa.R

paste -d ' ' ../../raw_data/level4/cd/aa/cd_aa.fam ../../raw_data/level4/cd/aa/toPlink_geno.ped > ../../raw_data/level5/cd/cd_aa.ped

### Batch 2
cut -d ' ' -f 1-6,8- ../../raw_data/level4/cd/ab/toPlink.ped > ../../raw_data/level4/cd/ab/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/cd/ab/toPlink_v2.ped > ../../raw_data/level4/cd/ab/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/cd_ab.R

paste -d ' ' ../../raw_data/level4/cd/ab/cd_ab.fam ../../raw_data/level4/cd/ab/toPlink_geno.ped > ../../raw_data/level5/cd/cd_ab.ped

cat ../../raw_data/level5/cd/cd_aa.ped ../../raw_data/level5/cd/cd_ab.ped > ../../raw_data/level6/cd.ped

### Subgroup 6
### Batch 1
cut -d ' ' -f 1-6,8- ../../raw_data/level4/cl/aa/toPlink.ped > ../../raw_data/level4/cl/aa/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/cl/aa/toPlink_v2.ped > ../../raw_data/level4/cl/aa/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/cl_aa.R

paste -d ' ' ../../raw_data/level4/cl/aa/cl_aa.fam ../../raw_data/level4/cl/aa/toPlink_geno.ped > ../../raw_data/level5/cl/cl_aa.ped

### Batch 2
cut -d ' ' -f 1-6,8- ../../raw_data/level4/cl/ab/toPlink.ped > ../../raw_data/level4/cl/ab/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/cl/ab/toPlink_v2.ped > ../../raw_data/level4/cl/ab/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/cl_ab.R

paste -d ' ' ../../raw_data/level4/cl/ab/cl_ab.fam ../../raw_data/level4/cl/ab/toPlink_geno.ped > ../../raw_data/level5/cl/cl_ab.ped

cat ../../raw_data/level5/cl/cl_aa.ped ../../raw_data/level5/cl/cl_ab.ped > ../../raw_data/level6/cl.ped

### Subgroup 7
### Batch 1
cut -d ' ' -f 1-6,8- ../../raw_data/level4/cy/aa/toPlink.ped > ../../raw_data/level4/cy/aa/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/cy/aa/toPlink_v2.ped > ../../raw_data/level4/cy/aa/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/cy_aa.R

paste -d ' ' ../../raw_data/level4/cy/aa/cy_aa.fam ../../raw_data/level4/cy/aa/toPlink_geno.ped > ../../raw_data/level5/cy/cy_aa.ped

### Batch 2
cut -d ' ' -f 1-6,8- ../../raw_data/level4/cy/ab/toPlink.ped > ../../raw_data/level4/cy/ab/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/cy/ab/toPlink_v2.ped > ../../raw_data/level4/cy/ab/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/cy_ab.R

paste -d ' ' ../../raw_data/level4/cy/ab/cy_ab.fam ../../raw_data/level4/cy/ab/toPlink_geno.ped > ../../raw_data/level5/cy/cy_ab.ped

cat ../../raw_data/level5/cy/cy_aa.ped ../../raw_data/level5/cy/cy_ab.ped > ../../raw_data/level6/cy.ped

### Subgroup 8
### Batch 1
cut -d ' ' -f 1-6,8- ../../raw_data/level4/dl/aa/toPlink.ped > ../../raw_data/level4/dl/aa/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/dl/aa/toPlink_v2.ped > ../../raw_data/level4/dl/aa/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/dl_aa.R

paste -d ' ' ../../raw_data/level4/dl/aa/dl_aa.fam ../../raw_data/level4/dl/aa/toPlink_geno.ped > ../../raw_data/level5/dl/dl_aa.ped

### Batch 2
cut -d ' ' -f 1-6,8- ../../raw_data/level4/dl/ab/toPlink.ped > ../../raw_data/level4/dl/ab/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/dl/ab/toPlink_v2.ped > ../../raw_data/level4/dl/ab/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/dl_ab.R

paste -d ' ' ../../raw_data/level4/dl/ab/dl_ab.fam ../../raw_data/level4/dl/ab/toPlink_geno.ped > ../../raw_data/level5/dl/dl_ab.ped

cat ../../raw_data/level5/dl/dl_aa.ped ../../raw_data/level5/dl/dl_ab.ped > ../../raw_data/level6/dl.ped

### Subgroup 9
### Batch 1
cut -d ' ' -f 1-6,8- ../../raw_data/level4/dy/aa/toPlink.ped > ../../raw_data/level4/dy/aa/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/dy/aa/toPlink_v2.ped > ../../raw_data/level4/dy/aa/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/dy_aa.R

paste -d ' ' ../../raw_data/level4/dy/aa/dy_aa.fam ../../raw_data/level4/dy/aa/toPlink_geno.ped > ../../raw_data/level5/dy/dy_aa.ped

### Batch 2
cut -d ' ' -f 1-6,8- ../../raw_data/level4/dy/ab/toPlink.ped > ../../raw_data/level4/dy/ab/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/dy/ab/toPlink_v2.ped > ../../raw_data/level4/dy/ab/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/dy_ab.R

paste -d ' ' ../../raw_data/level4/dy/ab/dy_ab.fam ../../raw_data/level4/dy/ab/toPlink_geno.ped > ../../raw_data/level5/dy/dy_ab.ped

cat ../../raw_data/level5/dy/dy_aa.ped ../../raw_data/level5/dy/dy_ab.ped > ../../raw_data/level6/dy.ped

### Subgroup 10
### Batch 1
cut -d ' ' -f 1-6,8- ../../raw_data/level4/ly/aa/toPlink.ped > ../../raw_data/level4/ly/aa/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/ly/aa/toPlink_v2.ped > ../../raw_data/level4/ly/aa/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/ly_aa.R

paste -d ' ' ../../raw_data/level4/ly/aa/ly_aa.fam ../../raw_data/level4/ly/aa/toPlink_geno.ped > ../../raw_data/level5/ly/ly_aa.ped

### Batch 2
cut -d ' ' -f 1-6,8- ../../raw_data/level4/ly/ab/toPlink.ped > ../../raw_data/level4/ly/ab/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/ly/ab/toPlink_v2.ped > ../../raw_data/level4/ly/ab/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/ly_ab.R

paste -d ' ' ../../raw_data/level4/ly/ab/ly_ab.fam ../../raw_data/level4/ly/ab/toPlink_geno.ped > ../../raw_data/level5/ly/ly_ab.ped

cat ../../raw_data/level5/ly/ly_aa.ped ../../raw_data/level5/ly/ly_ab.ped > ../../raw_data/level6/ly.ped

### Subgroup 11
### Batch 1
cut -d ' ' -f 1-6,8- ../../raw_data/level4/dly/aa/toPlink.ped > ../../raw_data/level4/dly/aa/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/dly/aa/toPlink_v2.ped > ../../raw_data/level4/dly/aa/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/dly_aa.R

paste -d ' ' ../../raw_data/level4/dly/aa/dly_aa.fam ../../raw_data/level4/dly/aa/toPlink_geno.ped > ../../raw_data/level5/dly/dly_aa.ped

### Batch 2
cut -d ' ' -f 1-6,8- ../../raw_data/level4/dly/ab/toPlink.ped > ../../raw_data/level4/dly/ab/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/dly/ab/toPlink_v2.ped > ../../raw_data/level4/dly/ab/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/dly_ab.R

paste -d ' ' ../../raw_data/level4/dly/ab/dly_ab.fam ../../raw_data/level4/dly/ab/toPlink_geno.ped > ../../raw_data/level5/dly/dly_ab.ped

### Batch 3
cut -d ' ' -f 1-6,8- ../../raw_data/level4/dly/ac/toPlink.ped > ../../raw_data/level4/dly/ac/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/dly/ac/toPlink_v2.ped > ../../raw_data/level4/dly/ac/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/dly_ac.R

paste -d ' ' ../../raw_data/level4/dly/ac/dly_ac.fam ../../raw_data/level4/dly/ac/toPlink_geno.ped > ../../raw_data/level5/dly/dly_ac.ped

cat ../../raw_data/level5/dly/dly_aa.ped ../../raw_data/level5/dly/dly_ab.ped ../../raw_data/level5/dly/dly_ac.ped > ../../raw_data/level6/dly.ped

### Subgroup 12
### Batch 1
cut -d ' ' -f 1-6,8- ../../raw_data/level4/cdly/aa/toPlink.ped > ../../raw_data/level4/cdly/aa/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/cdly/aa/toPlink_v2.ped > ../../raw_data/level4/cdly/aa/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/cdly_aa.R

paste -d ' ' ../../raw_data/level4/cdly/aa/cdly_aa.fam ../../raw_data/level4/cdly/aa/toPlink_geno.ped > ../../raw_data/level5/cdly/cdly_aa.ped

### Batch 2
cut -d ' ' -f 1-6,8- ../../raw_data/level4/cdly/ab/toPlink.ped > ../../raw_data/level4/cdly/ab/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/cdly/ab/toPlink_v2.ped > ../../raw_data/level4/cdly/ab/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/cdly_ab.R

paste -d ' ' ../../raw_data/level4/cdly/ab/cdly_ab.fam ../../raw_data/level4/cdly/ab/toPlink_geno.ped > ../../raw_data/level5/cdly/cdly_ab.ped

### Batch 3
cut -d ' ' -f 1-6,8- ../../raw_data/level4/cdly/ac/toPlink.ped > ../../raw_data/level4/cdly/ac/toPlink_v2.ped
cut -d ' ' -f 7- ../../raw_data/level4/cdly/ac/toPlink_v2.ped > ../../raw_data/level4/cdly/ac/toPlink_geno.ped

Rscript ../r/ProcessPlinkF90/cdly_ac.R

paste -d ' ' ../../raw_data/level4/cdly/ac/cdly_ac.fam ../../raw_data/level4/cdly/ac/toPlink_geno.ped > ../../raw_data/level5/cdly/cdly_ac.ped

cat ../../raw_data/level5/cdly/cdly_aa.ped ../../raw_data/level5/cdly/cdly_ab.ped ../../raw_data/level5/cdly/cdly_ac.ped > ../../raw_data/level6/cdly.ped

B.4 MakeBed.sh

Script:

# /data/tml_gpsm/cjgwx7/scripts/bash/

### Generate BED, BIM, and FAM files using PLINK software
### Exclude sex chromosomes (X and Y/19 and 20)
plink --ped ../../raw_data/level6/c.ped --map ../../raw_data/level6/global.map --out ../../raw_data/level7/c/c --make-bed --not-chr 19-20
plink --ped ../../raw_data/level6/d.ped --map ../../raw_data/level6/global.map --out ../../raw_data/level7/d/d --make-bed --not-chr 19-20
plink --ped ../../raw_data/level6/l.ped --map ../../raw_data/level6/global.map --out ../../raw_data/level7/l/l --make-bed --not-chr 19-20
plink --ped ../../raw_data/level6/y.ped --map ../../raw_data/level6/global.map --out ../../raw_data/level7/y/y --make-bed --not-chr 19-20
plink --ped ../../raw_data/level6/cd.ped --map ../../raw_data/level6/global.map --out ../../raw_data/level7/cd/cd --make-bed --not-chr 19-20
plink --ped ../../raw_data/level6/cl.ped --map ../../raw_data/level6/global.map --out ../../raw_data/level7/cl/cl --make-bed --not-chr 19-20
plink --ped ../../raw_data/level6/cy.ped --map ../../raw_data/level6/global.map --out ../../raw_data/level7/cy/cy --make-bed --not-chr 19-20
plink --ped ../../raw_data/level6/dl.ped --map ../../raw_data/level6/global.map --out ../../raw_data/level7/dl/dl --make-bed --not-chr 19-20
plink --ped ../../raw_data/level6/dy.ped --map ../../raw_data/level6/global.map --out ../../raw_data/level7/dy/dy --make-bed --not-chr 19-20
plink --ped ../../raw_data/level6/ly.ped --map ../../raw_data/level6/global.map --out ../../raw_data/level7/ly/ly --make-bed --not-chr 19-20
plink --ped ../../raw_data/level6/dly.ped --map ../../raw_data/level6/global.map --out ../../raw_data/level7/dly/dly --make-bed --not-chr 19-20
plink --ped ../../raw_data/level6/cdly.ped --map ../../raw_data/level6/global.map --out ../../raw_data/level7/cdly/cdly --make-bed --not-chr 19-20

B.5 QualityControl.sh

Script:

# /data/cjgwx7/tml_gpsm/scripts/bash/

### Filter by SNPs
### Subgroup 1
plink --bfile ../../raw_data/level7/c/c --out ../../intmd/input_data/c/c --make-bed --maf 0.01 --geno 0.1 --nonfounders

### Filter by pigs
plink --bfile ../../intmd/input_data/c/c --out ../../intmd/input_data/c/c --make-bed --mind 0.1 --nonfounders

### Subgroup 2
plink --bfile ../../raw_data/level7/d/d --out ../../intmd/input_data/d/d --make-bed --maf 0.01 --geno 0.1 --nonfounders
plink --bfile ../../intmd/input_data/d/d --out ../../intmd/input_data/d/d --make-bed --mind 0.1 --nonfounders

### Subgroup 3
plink --bfile ../../raw_data/level7/l/l --out ../../intmd/input_data/l/l --make-bed --maf 0.01 --geno 0.1 --nonfounders
plink --bfile ../../intmd/input_data/l/l --out ../../intmd/input_data/l/l --make-bed --mind 0.1 --nonfounders

### Subgroup 4
plink --bfile ../../raw_data/level7/y/y --out ../../intmd/input_data/y/y --make-bed --maf 0.01 --geno 0.1 --nonfounders
plink --bfile ../../intmd/input_data/y/y --out ../../intmd/input_data/y/y --make-bed --mind 0.1 --nonfounders

### Subgroup 5
plink --bfile ../../raw_data/level7/cd/cd --out ../../intmd/input_data/cd/cd --make-bed --maf 0.01 --geno 0.1 --nonfounders
plink --bfile ../../intmd/input_data/cd/cd --out ../../intmd/input_data/cd/cd --make-bed --mind 0.1 --nonfounders

### Subgroup 6
plink --bfile ../../raw_data/level7/cl/cl --out ../../intmd/input_data/cl/cl --make-bed --maf 0.01 --geno 0.1 --nonfounders
plink --bfile ../../intmd/input_data/cl/cl --out ../../intmd/input_data/cl/cl --make-bed --mind 0.1 --nonfounders

### Subgroup 7
plink --bfile ../../raw_data/level7/cy/cy --out ../../intmd/input_data/cy/cy --make-bed --maf 0.01 --geno 0.1 --nonfounders
plink --bfile ../../intmd/input_data/cy/cy --out ../../intmd/input_data/cy/cy --make-bed --mind 0.1 --nonfounders

### Subgroup 8
plink --bfile ../../raw_data/level7/dl/dl --out ../../intmd/input_data/dl/dl --make-bed --maf 0.01 --geno 0.1 --nonfounders
plink --bfile ../../intmd/input_data/dl/dl --out ../../intmd/input_data/dl/dl --make-bed --mind 0.1 --nonfounders

### Subgroup 9
plink --bfile ../../raw_data/level7/dy/dy --out ../../intmd/input_data/dy/dy --make-bed --maf 0.01 --geno 0.1 --nonfounders
plink --bfile ../../intmd/input_data/dy/dy --out ../../intmd/input_data/dy/dy --make-bed --mind 0.1 --nonfounders

### Subgroup 10
plink --bfile ../../raw_data/level7/ly/ly --out ../../intmd/input_data/ly/ly --make-bed --maf 0.01 --geno 0.1 --nonfounders
plink --bfile ../../intmd/input_data/ly/ly --out ../../intmd/input_data/ly/ly --make-bed --mind 0.1 --nonfounders

### Subgroup 11
plink --bfile ../../raw_data/level7/dly/dly --out ../../intmd/input_data/dly/dly --make-bed --maf 0.01 --geno 0.1 --nonfounders
plink --bfile ../../intmd/input_data/dly/dly --out ../../intmd/input_data/dly/dly --make-bed --mind 0.1 --nonfounders

### Subgroup 12
plink --bfile ../../raw_data/level7/cdly/cdly --out ../../intmd/input_data/cdly/cdly --make-bed --maf 0.01 --geno 0.1 --nonfounders
plink --bfile ../../intmd/input_data/cdly/cdly --out ../../intmd/input_data/cdly/cdly --make-bed --mind 0.1 --nonfounders

B.6 MakeGRMs.sh

Script:

# /data/cjgwx7/tml_gpsm/scripts/bash/

### Make Genomic Relationship Matrix for each subset

gcta64 --bfile ../../intmd/input_data/c/c --make-grm --out ../../intmd/grms/c/c_all --thread-num 24
gcta64 --bfile ../../intmd/input_data/d/d --make-grm --out ../../intmd/grms/d/d_all --thread-num 24
gcta64 --bfile ../../intmd/input_data/l/l --make-grm --out ../../intmd/grms/l/l_all --thread-num 24
gcta64 --bfile ../../intmd/input_data/y/y --make-grm --out ../../intmd/grms/y/y_all --thread-num 24
gcta64 --bfile ../../intmd/input_data/cd/cd --make-grm --out ../../intmd/grms/cd/cd_all --thread-num 24
gcta64 --bfile ../../intmd/input_data/cl/cl --make-grm --out ../../intmd/grms/cl/cl_all --thread-num 24
gcta64 --bfile ../../intmd/input_data/cy/cy --make-grm --out ../../intmd/grms/cy/cy_all --thread-num 24
gcta64 --bfile ../../intmd/input_data/dl/dl --make-grm --out ../../intmd/grms/dl/dl_all --thread-num 24
gcta64 --bfile ../../intmd/input_data/dy/dy --make-grm --out ../../intmd/grms/dy/dy_all --thread-num 24
gcta64 --bfile ../../intmd/input_data/ly/ly --make-grm --out ../../intmd/grms/ly/ly_all --thread-num 24
gcta64 --bfile ../../intmd/input_data/dly/dly --make-grm --out ../../intmd/grms/dly/dly_all --thread-num 24
gcta64 --bfile ../../intmd/input_data/cdly/cdly --make-grm --out ../../intmd/grms/cdly/cdly_all --thread-num 24