Entering edit mode
5.8 years ago
aarvaBioinfo
▴
10
Hi all, I want to create a hapmap file for multi samples by using each samples genomic VCF file columns information as CHROME, POS, REF and ALT. Is anyone has idea about this using some script programs. here is my gVCF file examples:
Sample1.gvcf
Chr01 36230803 . T <*> 0 . DP=19;I16=10,9,0,0,734,28854,0,0,703,26011,0,0,440,10622,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,57,255:19,0
Chr01 36262603 . C <*> 0 . DP=17;I16=6,10,0,0,656,26896,0,0,302,10512,0,0,344,8136,0,0;QS=1,0;MQSB=0.863243;MQ0F=0.411765 PL:AD 0,48,214:16,0
Chr01 36329877 . G <*> 0 . DP=10;I16=5,4,0,0,355,14177,0,0,333,12321,0,0,195,4463,0,0;QS=1,0;MQSB=0.974597;MQ0F=0 PL:AD 0,27,238:9,0
Chr01 36362260 . C <*> 0 . DP=47;I16=23,23,0,0,1797,70989,0,0,251,2951,0,0,1031,24791,0,0;QS=1,0;MQSB=0.580141;MQ0F=0.510638 PL:AD 0,138,56:46,0
Chr01 36393636 . C <*> 0 . DP=29;I16=15,14,0,0,1164,46844,0,0,1073,39701,0,0,599,13899,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,87,255:29,0
Chr01 36516702 . T <*> 0 . DP=26;I16=11,14,0,0,973,38199,0,0,220,5796,0,0,543,12957,0,0;QS=1,0;MQSB=0.847716;MQ0F=0.653846 PL:AD 0,75,144:25,0
Chr01 36548162 . T <*> 0 . DP=11;I16=3,7,0,0,393,15529,0,0,370,13690,0,0,246,6058,0,0;QS=1,0;MQSB=0.916482;MQ0F=0 PL:AD 0,30,249:10,0
Chr01 36563397 . G <*> 0 . DP=16;I16=13,3,0,0,634,25320,0,0,592,21904,0,0,306,6660,0,0;QS=1,0;MQSB=1;MQ0F=0 PL:AD 0,48,255:16,0
in this file i have no GT information.
