vcf at variable sites only

Question

[samuel.lipworth]

Hi,

I have a vcf file which simply gives the call at every single position eg:

L=C;BaseCounts=4,131,2,5;BaseCounts4=0,92,0,0;DM4=0.037;DM4L=-2.134;DP=147;DP4=47,45,0,0;DPT4L=-14.831;DZ4=0.052;DZ4L=-2.141;GC=57.430;MQ=60;MQ4=60;PCALL4=1.000;PCONS4=1.000;SBR=0 GT:DP   0/0:92
R00000039   7336    .   T   .   272.00  PASS    ABQ4=34.976;BCALL=T;BaseCounts=6,9,2,125;BaseCounts4=0,0,0,84;DM4=-0.262;DM4L=-2.668;DP=147;DP4=44,40,0,0;DPT4L=-22.831;DZ4=-0.216;DZ4L=-2.621;GC=57.430;MQ=60;MQ4=60;PCALL4=1.000;PCONS4=1.000;SBR=0   GT:DP   0/0:84
R00000039   7337    .   C   .   273.00  PASS    ABQ4=34.960;BCALL=C;BaseCounts=5,134,1,1;BaseCounts4=0,100,0,0;DM4=0.337;DM4L=-1.599;DP=147;DP4=50,50,0,0;DPT4L=-6.831;DZ4=0.320;DZ4L=-1.662;GC=57.430;MQ=60;MQ4=60;PCALL4=1.000;PCONS4=1.000;SBR=0 GT:DP   0/0:100
R00000039   7338    .   G   .   273.00  PASS    ABQ4=35.309;BCAL

How can I turn this into a vcf file which only calls at variable positions eg

CHROM    POS    REF    ALT    
R00000039    73    A    T

Answer 1

[samuel.lipworth]

Grep is the answer, sorry please close this question!

[WouterDeCoster]

Good job on figuring it out yourself. Feel free to edit your answer with the exact command you ran to solve this and mark your question as accepted. There is no need to close.