Mercurial > repos > jjohnson > pileup_to_vcf

comparison pileup_to_vcf.py @ 7:e77ab15bbce9

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Fix VCF header
author Jim Johnson <jj@umn.edu>
date Wed, 20 Mar 2013 07:50:38 -0500
parents d90f56ecd2f9
children c0a6e8f595ec
comparison
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6:d90f56ecd2f9 7:e77ab15bbce9
34 34
35 vcf_header = """\ 35 vcf_header = """\
36 ##fileformat=VCFv4.0 36 ##fileformat=VCFv4.0
37 ##source=pileup_to_vcf.pyV1.1 37 ##source=pileup_to_vcf.pyV1.1
38 ##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\"> 38 ##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">
39 ##INFO=<ID=$SAF_header,Number=.,Type=Float,Description=\"Specific Allele Frequency\"> 39 ##INFO=<ID=SAF,Number=.,Type=Float,Description=\"Specific Allele Frequency\">
40 ##FILTER=<ID=DP,Description=\"Minimum depth of %s\"> 40 ##FILTER=<ID=DP,Description=\"Minimum depth of %s\">
41 ##FILTER=<ID=$SAF_header,Description=\"Allele frequency of at least %s with base quality minimum %d\"> 41 ##FILTER=<ID=SAF,Description=\"Allele frequency of at least %s with base quality minimum %d\">
42 #CHROM POS ID REF ALT QUAL FILTER INFO\ 42 #CHROM POS ID REF ALT QUAL FILTER INFO\
43 """ 43 """
44 44
45 def __main__(): 45 def __main__():
46 #Parse Command Line 46 #Parse Command Line