Comparison Between O.lurida WT and Hatchery Genetics

Project Goal

Compare genetic variation between hatchery and wild type O Lurida My end goal is a nice comparision and maybe a visual

Many times a specific location in the genome is covered by sequence reads for sample 01

samtools depth \
/home/shared/8TB_HDD_02/thielkla/Karina-chinook/CSBM18H/CSMB18H.01.bam \
> /home/shared/8TB_HDD_02/thielkla/Karina-chinook/CSBM18H/CSMB18H.depth
-The head of the depth file using {bash}
head /home/shared/8TB_HDD_02/thielkla/Karina-chinook/CSBM18H/CSMB18H.depth
-gives
Contig0 229 1
Contig0 230 1
Contig0 231 1
Contig0 232 1
Contig0 233 1
Contig0 234 1
Contig0 235 1
Contig0 236 1
Contig0 237 1
Contig0 238 1

I want to see if allele frequencies differ between populations

• I call varients for 5 of my hatchery BAM files

for i in {01..05}; do
  /home/shared/bcftools-1.14/bcftools mpileup -Ou -f \
  /home/shared/8TB_HDD_02/thielkla/Karina-chinook/Olurida_v081.fa \
  /home/shared/8TB_HDD_02/thielkla/Karina-chinook/CSBM18H/CSMB18H.${i}.bam \
  | /home/shared/bcftools-1.14/bcftools call -mv -Ov -o \
  /home/shared/8TB_HDD_02/thielkla/Karina-chinook/outputv2/H${i}.vcf
done

• call varients for wildtype

for i in {01..05}; do
  /home/shared/bcftools-1.14/bcftools mpileup -Ou -f \
  /home/shared/8TB_HDD_02/thielkla/Karina-chinook/Olurida_v081.fa \
  /home/shared/8TB_HDD_02/thielkla/Karina-chinook/CSMB17W/CSMB17W.${i}.bam \
  | /home/shared/bcftools-1.14/bcftools call -mv -Ov -o \
  /home/shared/8TB_HDD_02/thielkla/Karina-chinook/outputv2/H${i}.vcf
done