charr_dosaf

cd /home/tkess/scratch/CharrGDL_WG
module load htslib
module load samtools

#this is with 2pops - PALE
/home/tkess/angsd/angsd \
  -anc /home/tkess/scratch/CharrGDL_WG/Charr_Genome/GCA_002910315.2_ASM291031v2_genomic.fasta \
  -bam PALEbams.txt \
  -out PALE \
  -dosaf 1 \
  -GL 1 \
  -doCounts 1 \
  -nThreads 20 \
  -minMapQ 30 \
  -minQ 20 \
  -minInd 10 \
  -doMajorMinor 5 \
  -doMaf 2 \
  -setMinDepth 10 \
  -uniqueOnly 1 \
  -remove_bads 1 \
  -only_proper_pairs 1 \
  -maxDepth 400 \
  -rf charr_chroms.txt

#this is with 2pops - DARK
/home/tkess/angsd/angsd \
  -anc /home/tkess/scratch/CharrGDL_WG/Charr_Genome/GCA_002910315.2_ASM291031v2_genomic.fasta \
  -bam DARKbams.txt \
  -out DARK \
  -dosaf 1 \
  -GL 1 \
  -doCounts 1 \
  -nThreads 20 \
  -minMapQ 30 \
  -minQ 20 \
  -minInd 10 \
  -doMajorMinor 5 \
  -doMaf 2 \
  -setMinDepth 10 \
  -uniqueOnly 1 \
  -remove_bads 1 \
  -only_proper_pairs 1 \
  -maxDepth 400 \
  -rf charr_chroms.txt