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
Grep is the answer, sorry please close this question!
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.
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