charr_angsd2beagle_repfiltered

## Load software modules
module load angsd

cd /home/tkess/scratch/CharrGDL_WG

angsd -GL 1 \
  -nThreads 20 \
  -doGlf 2 \
  -minMapQ 30 \
  -minQ 20 \
  -minInd 10 \
  -out Charr_paledark_realign_norep_maf05 \
  -doMajorMinor 1 \
  -doMaf 2 \
  -SNP_pval 2e-6 \
  -doCounts 1 \
  -dumpCounts 2 \
  -doQsDist 1 \
  -setMinDepth 20 \
  -uniqueOnly 1 \
  -remove_bads 1 \
  -only_proper_pairs 1 \
  -maxDepth 800 \
  -bam Realignedbams.txt \
  -rf charr_chroms.txt \
  -sites pcangsd_sites_norep_CM.tsv \
  -minMaf 0.05