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vcf2gvf.py fails with missing INFO field #21

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cfljam opened this issue May 20, 2014 · 1 comment
Open

vcf2gvf.py fails with missing INFO field #21

cfljam opened this issue May 20, 2014 · 1 comment
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@cfljam
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cfljam commented May 20, 2014

Code relies on INFO field being present and fails in cases like:

comp20364_c0_seq1   2   .   GGT CTTCTCTGGT  35.3186 .   .   GT:DP:RO:QR:AO:QA:G

Giving

/Users/johnmccallum/Dropbox/BSA_RNASEQ/HRM_design_2/galaxy-pcr-markers/vcf2gvf.py in <module>()
     52             if info_field[0]=='INDEL':
     53                 info_field[0]="TYPE=INDEL"
---> 54             info_dict=dict(X.split('=') for X in info_field)
     55             ##if no TYPE key, then add TYPE=SNP for samtools case
     56             if not info_dict.has_key('TYPE'):

ValueError: dictionary update sequence element #0 has length 1; 2 is required

@cfljam cfljam self-assigned this May 20, 2014
@cfljam
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cfljam commented May 20, 2014

This is a pathological case due to vcftools being run without --recode-INFO-all flag

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