Perfect 👍 — I’ll show you exactly how to extract and store:

✅ SNP-only, biallelic VCF ✅ PLINK bed/bim/fam set

starting only from:

• sorted.bam
• reference: /home/user/Desktop/Syncthing/Syncthing_pc/genomics/references/hs38d1s_nochr.fa

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🧬 STEP 1 — Create Variant-Only SNP+INDEL VCF

(This is the base file we derive everything from)

bcftools mpileup \
  -f /home/user/Desktop/Syncthing/Syncthing_pc/genomics/references/hs38d1s_nochr.fa \
  sorted.bam | \
bcftools call -m -v -Oz -o clinical_raw.vcf.gz

Index:

tabix -p vcf clinical_raw.vcf.gz

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🧬 STEP 2 — Filter to High-Quality Variants

bcftools filter -Oz -o clinical.vcf.gz \
  -e 'QUAL<20 || DP<10' clinical_raw.vcf.gz

tabix -p vcf clinical.vcf.gz

Now you have:

clinical.vcf.gz (SNP + INDEL, high quality)

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🧬 STEP 3 — Extract SNP-Only

bcftools view -v snps clinical.vcf.gz -Oz -o snps_only.vcf.gz
tabix -p vcf snps_only.vcf.gz

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🧬 STEP 4 — Keep Only Biallelic SNPs

(critical for PLINK & ancestry)

bcftools view -m2 -M2 snps_only.vcf.gz -Oz -o ancestry.vcf.gz
tabix -p vcf ancestry.vcf.gz

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✅ You now have your MASTER ancestry VCF:

ancestry.vcf.gz
ancestry.vcf.gz.tbi

Size: ~200–600 MB This is your long-term archive.

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🧬 STEP 5 — Convert to PLINK Format

plink --vcf ancestry.vcf.gz --make-bed --out mygenome

This creates:

mygenome.bed
mygenome.bim
mygenome.fam

Size: ~150–400 MB

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📦 What to Store Long-Term

Keep:

ancestry.vcf.gz
ancestry.vcf.gz.tbi
mygenome.bed
mygenome.bim
mygenome.fam

That’s it.

You can delete:

• clinical_raw.vcf.gz
• intermediate files
• giant all-sites VCF
• BAM (if ancestry-only forever)

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🧠 Why This Is Future-Proof

From ancestry.vcf.gz you can:

Extract 23andMe SNPs

bcftools view -R 23andme_positions.bed ancestry.vcf.gz

Extract AADR 1240K

plink --bfile mygenome --extract 1240k_snps.txt --make-bed --out aadr

Extract any company's panel

Just subset SNP list.

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🟢 Final Storage Size Comparison

File	Size
BAM	30–90 GB
CRAM	10–25 GB
SNP-only VCF	200–600 MB
PLINK set	150–400 MB

👉 ~100× smaller than BAM.

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If you want, I can now:

• Create a single one-shot script
• Validate strand orientation vs 1240K
• Show how to make mock 23andMe file

Tell me your next target 👍