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chapmanb / bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure
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problem #35

Open karthickji opened 1 year ago

karthickji commented 1 year ago

this is my vcf file i don't understand MAXGT and POLY. how to remove MAXGT AND POLY, i am go to gwas study but thia MAXGT AND POLY was my problem . pls any one help me <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">

##fileformat=VCFv4.1 |   |   |   |   |   |   |   |   |   |   -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- ##fileDate=20130319 |   |   |   |   |   |   |   |   |   |   ##source=GenerateReportDataAndVCFv2.2.2.0 |   |   |   |   |   |   |   |   |   |   ##reference=HumanNCBI37_UCSC |   |   |   |   |   |   |   |   |   |   ##phasing=none |   |   |   |   |   |   |   |   |   |   ##INFO= |   |   |   |   |   |   |   |   |   |   ##INFO= |   |   |   |   |   |   |   |   |   |   ##INFO= |   |   |   |   |   |   |   |   |   |   ##INFO= |   |   |   |   |   |   |   |   |   |   ##INFO= |   |   |   |   |   |   |   |   |   |   ##FILTER= |   |   |   |   |   |   |   |   |   |   ##FORMAT= |   |   |   |   |   |   |   |   |   |   ##FORMAT= |   |   |   |   |   |   |   |   |   |   #CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | 12AD50320_MAXGT | 12AD50320_POLY chr16 | 60054 | rs62028702 | A | C | 23 | PASS | DP=9 | GT:GQ | 0/1:23 | 0/1:56 chr16 | 60087 | rs62028703 | C | G | 27 | PASS | DP=13 | GT:GQ | 0/1:27 | 0/1:60 chr16 | 60095 | rs62028704 | G | T | 26 | PASS | DP=13 | GT:GQ | 0/1:26 | 0/1:59 chr16 | 60120 | . | G | A | 11 | q20 | DP=10 | GT:GQ | 1/0:11 | 1/0:43