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Installation: The python vcf module uses the yapps library (http://pypi.python.org/pypi/Yapps2/2.0.4) to generate a parser (vcfparser.py) for parsing vcf fields. To generate the parser, simply run: make -f vcf.mk Then, using the parser in your code is as easy as: import vcf vcf.parse('genotype', '0/0:23,0,0:23:60:0,60,709,60,709,709') >>> {'AD': [23, 0, 0], 'DP': 23, 'GQ': 60, 'GT': ((0, 0), False), 'PL': [0, 60, 709, 60, 709, 709]} vcf.parse('info', 'AC=1;AF=0.042;AN=24;BaseQRankSum=1.008;DP=280;Dels=0.00;FS=2.163;HaplotypeScore=1.0714;InbreedingCoeff=-0.0452;MLEAC=1;MLEAF=0.042;MQ=59.92;MQ0=0;MQRankSum=-0.875;QD=8.58;ReadPosRankSum=0.314;SB=-1.641e-02;VQSLOD=5.1338;culprit=QD') >>> {'AC': 1, 'AF': 0.042, 'AN': 24, 'BaseQRankSum': 1.008, 'DP': 280, 'Dels': 0.0, 'FS': 2.163, 'HaplotypeScore': 1.0714, 'InbreedingCoeff': -0.0452, 'MLEAC': 1, 'MLEAF': 0.042, 'MQ': 59.92, 'MQ0': 0, 'MQRankSum': -0.875, 'QD': 8.58, 'ReadPosRankSum': 0.314, 'SB': -0.01641, 'VQSLOD': 5.1338, 'culprit': 'QD'} To see other things you can parse, look at the rules in vcfparser.g that look like: rule info: ( ... ) END
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Python library for parsing/handling VCF files
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