The NR and NV tag in vcf file

[繼武吳]

Excuse me,

I have used platypus tools to call snp and indel.

However, I have a question for my result.

The following is one row of my result.

I found that the result NR=0 and NV=0 and genotype=./.  could be happened. And does this mean the indel does not exist?

chr2 7489055 . AAAGG A 324 SC;HapScore;MQ;QD BRF=0.45;FR=0.5000;HP=2;HapScore=8;MGOF=34;MMLQ=100;MQ=0;NF=0;NR=0;PP=324;QD=0;SC=AAGGAAGGAGAAAGGAAGGAA;SbPval=1.0;Source=Platypus;TC=0;TCF=0;TCR=0;TR=0;WE=7489067;WS=7489032 GT:GL:GOF:GQ:NR:NV   ./.:-35.22,0.0,-3.65:34:36:0:0

Thanks a lot

[Andy Rimmer]

Was this calling on just the one sample? Or is this just a sub-set of a larger VCF with multiple samples?

Andy

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?

[繼武吳]

The calling was on just one sample. I found about 1000 variants which are like that ( NV=0, NR>=0 , genotype = ./. and any other ) for one sample.

And how should I interpret it?

as the following,  NV=0, and the calling  are indel , why?

Thanks a lot for solve my problems

chr2 154687487 . A AT 22 QD;alleleBias BRF=0.05;FR=0.9998;HP=20;HapScore=2;MGOF=5;MMLQ=100;MQ=47.12;NF=0;NR=0;PP=22;QD=0;SC=TGACAGGCTCATTTTTTTTTT;SbPval=1.0;Source=Platypus;TC=14;TCF=7;TCR=7;TR=0;WE=154687495;WS=154687477 GT:GL:GOF:GQ:NR:NV 1/1:-2.2,-0.31,0.0:5:5:14:0

chr2 156073655 . T TA 11 Q20;QD;alleleBias BRF=0.06;FR=0.9994;HP=20;HapScore=2;MGOF=3;MMLQ=100;MQ=47.12;NF=0;NR=0;PP=11;QD=0;SC=AAACTGTTGGTAAAAAAAAAA;SbPval=1.0;Source=Platypus;TC=11;TCF=6;TCR=5;TR=0;WE=156073663;WS=156073645 GT:GL:GOF:GQ:NR:NV 1/0:-1.13,0.0,-0.03:3:3:11:0

chr2 157807854 . T TGG 18 Q20;MQ;QD BRF=0.18;FR=0.9999;HP=11;HapScore=2;MGOF=15;MMLQ=100;MQ=33.24;NF=0;NR=0;PP=18;QD=0;SC=TATAATAATTTGGGGGGGGGG;SbPval=1.0;Source=Platypus;TC=1;TCF=1;TCR=0;TR=0;WE=157807862;WS=157807844 GT:GL:GOF:GQ:NR:NV ./.:-2.6,-0.34,0.0:15:5:1:0

Andy Rimmer於 2016年6月15日星期三 UTC+8下午11時56分46秒寫道：