I am running VCFtools. My input file looks like this:

NW_0148388.1  404     .       A       G       225     .       DP=15;VDB=0.310396;SGB=-0.686358;MQSB=0.640197;MQ0F=0;AC=2;AN=2;DP4=0,0,7,7;MQ=43       GT:PL   1/1:255,42,0
NW_0148388.1  495     .       T       C       225     .       DP=16;VDB=0.351783;SGB=-0.689466;MQSB=0.948436;MQ0F=0;AC=2;AN=2;DP4=0,0,6,10;MQ=39      GT:PL   1/1:255,48,0
NW_0148388.1  540     .       T       G       225     .       DP=16;VDB=0.909865;SGB=-0.688148;MQSB=0.959011;MQ0F=0;AC=2;AN=2;DP4=0,0,8,7;MQ=41       GT:PL   1/1:255,45,0
NW_0148388.1  745     .       G       A       225     .       DP=24;VDB=0.680279;SGB=-0.692352;MQSB=0.769328;MQ0F=0;AC=2;AN=2;DP4=0,0,8,13;MQ=40      GT:PL   1/1:255,63,0

After I run:

vcftools --gzvcf MQ40_M2_edit.vcf  --thin 50000  --recode --recode-INFO-all --out thin50K_M2 

The output looks like this:

NW_0148388.1  540     .       T       G       225     .       DP=16;VDB=0.909865;SGB=-0.688148;MQSB=0.959011;MQ0F=0;AC=2;AN=2;DP4=0,0,8,7;MQ=41       GT:PL
NW_0148388.1  51538   .       T       C       225     .       DP=17;VDB=0.965004;SGB=-0.689466;MQSB=0.987669;MQ0F=0;AC=2;AN=2;DP4=0,0,8,8;MQ=40       GT:PL
NW_0148388.1  101704  .       T       C       225     .       DP=34;VDB=0.8046;SGB=-0.692976;MQSB=0.705431;MQ0F=0;AC=2;AN=2;DP4=0,0,17,9;MQ=40        GT:PL
NW_0148388.1  154423  .       C       T       225     .       DP=17;VDB=0.614965;SGB=-0.686358;MQSB=0.997503;MQ0F=0;AC=2;AN=2;DP4=0,0,10,4;MQ=40      GT:PL

It cuts off everything after "GT:PL" which contains important info. When i run other filters with the same code all the info remains. Is there a way to retain all this info?