Entering edit mode
3.3 years ago
JBC
•
0
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?
