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SNP_filtering.md

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SNP filtering and imputation

Dependencies

  • beagle 5.4 (beagle.22Jul22.46e.jar)
  • bgzip v1.13+ds
  • tabix v1.13+ds
  • plink v2.00a3.7LM
  • split_vcf.py (local)

Prepare location

export CPU=16

Run filtering ( MAP >= 0.05 and HW >= 10^-8 )

bgzip -d -c populations.snps.vcf.gz | awk '$1 ~ /^#/ {print $0;next} {print $0 | "sort -k1,1V -k2,2n"}' > populations.snps.vcf
plink2 --thread-num ${CPU} --vcf populations.snps.vcf --make-bed --allow-extra-chr --no-sex --max-alleles 2 --out tmp1
plink2 --bfile tmp1 --maf 0.05 --hwe 0.000000001 --make-bed --allow-extra-chr --no-sex --out tmp2
plink2 --bfile tmp2 --recode vcf --allow-extra-chr --no-sex --out populations.hwe
rm -f tmp* populations.snps.vcf

Run imputation

## Remove chromosomes with single SNP
scripts/split_vcf.py -in populations.hwe.vcf -out populations.no_singleton.vcf
## Genotype imputation: Beagle GT
bgzip -l9 populations.no_singleton.vcf
java -jar beagle.22Jul22.46e.jar gt=populations.no_singleton.vcf.gz out=populations.imputed
## Add chromosome with single SNP
bgzip -d populations.imputed.vcf.gz
scripts/split_vcf.py -in populations.hwe.vcf --imputed populations.imputed.vcf -out mussels.snps.vcf

## Tidy
rm -f populations.hwe.vcf populations.no_singleton.vcf populations.imputed.vcf populations.no_singleton.vcf.gz populations.*.log
bgzip -l9 mussels.snps.vcf
tabix -h mussels.snps.vcf.gz

Final artefacts

  • mussels.snps.vcf.gz
  • mussels.snps.vcf.gz.tbi