Mercurial > repos > jjohnson > pileup_to_vcf
comparison pileup_to_vcf.py @ 6:d90f56ecd2f9
Change version to: pileup_to_vcf.pyV1.1
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 20 Mar 2013 07:30:20 -0500 |
| parents | fafa105e5f58 |
| children | e77ab15bbce9 |
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| 5:8688e29ba96f | 6:d90f56ecd2f9 |
|---|---|
| 32 import optparse | 32 import optparse |
| 33 from optparse import OptionParser | 33 from optparse import OptionParser |
| 34 | 34 |
| 35 vcf_header = """\ | 35 vcf_header = """\ |
| 36 ##fileformat=VCFv4.0 | 36 ##fileformat=VCFv4.0 |
| 37 ##source=pileup_to_vcf.pyV1.0 | 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_header,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_header,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\ |