VCF manipulation with GATK

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VCF manipulation with GATK

原文日期: 2017-09-07
来源: https://github.com/wlz0726/wlz0726.github.io

GATK VCF 操作

选择变异

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# 选择 SNP
gatk SelectVariants \
  -V input.vcf \
  --select-type-to-include SNP \
  -O snps.vcf

# 选择 INDEL
gatk SelectVariants \
  -V input.vcf \
  --select-type-to-include INDEL \
  -O indels.vcf

# 选择特定样本
gatk SelectVariants \
  -V input.vcf \
  -sn sample1 \
  -O sample1.vcf

合并 VCF

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gatk MergeVcfs \
  -I input1.vcf \
  -I input2.vcf \
  -O merged.vcf

拆分 VCF

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# 按染色体拆分
for chr in {1..22} X Y; do
  gatk SelectVariants \
    -V input.vcf \
    -R reference.fasta \
    -L $chr \
    -O chr${chr}.vcf
done

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