22 lines
775 B
Python
22 lines
775 B
Python
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import vcf
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# 打开 VCF 文件
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vcf_reader = vcf.Reader(open('your_input.vcf', 'r'))
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# 打开输出 VCF 文件
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vcf_writer = vcf.Writer(open('output.vcf', 'w'), vcf_reader)
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# 遍历 VCF 文件中的每个记录
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for record in vcf_reader:
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if 'STATUS' in record.INFO and (
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'StrongSomatic' in record.INFO['STATUS'] or 'LikelySomatic' in record.INFO['STATUS']):
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# 获取实验样本和对照样本的 AF 频率
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experimental_af = record.genotype('experimental_sample')['AF']
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control_af = record.genotype('control_sample')['AF']
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# 检查实验样本的 AF 是否大于对照样本
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if experimental_af > control_af:
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vcf_writer.write_record(record)
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# 关闭输出 VCF 文件
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vcf_writer.close()
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