Workflow

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📥 Input

• VCF file: 169.vcf.gz

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🔄 VCF to Matrix

🔧 Script: vcftomatrix.sh

invcf=169.vcf.gz
pref=169

mkdir -p $pref

bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%TGT]\n' $invcf | \
  tr "|" "/" | \
  tr -d "/" | \
  sed "s:chr0\\?::" | \
  awk -v OFS="\t" '{$1 = $1 + 0; print $0}' > ${pref}/mat_vcf.txt

cut -f1-4 $pref/mat_vcf.txt > $pref/pos.txt

# The following fails for some reason (grep CHR part)
bcftools view -o - -h $invcf | \
  grep CHR | \
  tr "\t" "\n" | \
  tail -n +10 > $pref/sample_list.txt

📤 Output Files

• pos.txt
• sample_list.txt
• mat_vcf.txt

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🔄 Matrix to HDF5

▶️ Command

./make_HDF_dataset.sh <input-dir> <output-prefix>

Example:

./make_HDF_dataset.sh /home/scratch3/169 169

📤 Output File

• 169_transp.h5

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