Question: VCF quaility score/filter assessment for ICGC vcf (by sanger pipeline)
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gravatar for morovatunc
2.8 years ago by
morovatunc400
Turkey
morovatunc400 wrote:

Hi,

I am analyzing vcf files from ICGC which were called by sanger pipeline. During this analyses QUALITY column in the vcf is "." The suggestions here are not included. However, there are CaveMan info files given.

INFO=ID=MP,Number=1,Type=Float,Description="Sum of CaVEMan somatic genotype probabilities"> INFO=ID=GP,Number=1,Type=Float,Description="Sum of CaVEMan germline genotype probabilities"> INFO=ID=TG,Number=1,Type=String,Description="Most probable genotype as called by CaVEMan" INFO=ID=TP,Number=1,Type=Float,Description="Probability of most probable genotype as called by CaVEMan"> INFO=ID=SG,Number=1,Type=String,Description="2nd most probable genotype as called by CaVEMan"> INFO=ID=SP,Number=1,Type=Float,Description="Probability of 2nd most probable genotype as called by CaVEMan"> INFO=<id=ds,number=.,type=string,description="dbsnp id="" of="" known="" snp"="">

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOUR 1 10109 c85b77e0-2464-11e5-a4df-7335283a0828
A T . SR;MN;MQ;HSD;VUM;MNP
DP=369;MP=1.0e+00;GP=7.0e-25;TG=AA/AT;TP=1.0e+00;SG=AA/AA;SP=2.2e-11
GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:103:0:0:9:60:0:0:1:5.8e-02 0|1:98:0:0:10:86:0:0:2:6.1e-02

I also have an another assessment, could you please point out a source to interpret filters. For example, this specific filter is not presented in the first mutation but it is presented. Does this mean in the second mutation it has that property so that it contains that filter or it does not contain that filter so it was filtered by that filter? so having a filter means it merits that property or not?

FILTER=<id=vum,description="position has="" &gt;="3" mutant="" allele="" present="" in="" at="" least="" 1="" percent="" unmatched="" normal="" samples="" in="" the="" unmatched="" vcf."="">

1 10109 c85b77e0-2464-11e5-a4df-7335283a0828 A T
. SR;MN;MQ;HSD;VUM;MNP
DP=369;MP=1.0e+00;GP=7.0e-25;TG=AA/AT;TP=1.0e+00;SG=AA/AA;SP=2.2e-11
GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:103:0:0:9:60:0:0:1:5.8e-02 0|1:98:0:0:10:86:0:0:2:6.1e-02

1 10328 c85b835c-2464-11e5-a4df-7335283a0828 A T
. SR;MN;HSD;VUM;MNP
DP=186;MP=1.0e+00;GP=1.8e-11;TG=AA/AT;TP=1.0e+00;SG=AA/AA;SP=2.9e-07
GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM 0|0:4:0:0:0:60:0:0:4:5.9e-02
0|1:13:0:0:0:97:0:0:8:6.8e-0

I appreciate every single word of an information

Best regards,

Tunc.

vcf • 905 views
ADD COMMENTlink written 2.8 years ago by morovatunc400
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