Question: Creation of hapmap format file for multi samples using individual sample gVCF file REF/ALT info
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2.0 years ago by
aarvaBioinfo10
aarvaBioinfo10 wrote:

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.

snp • 462 views
ADD COMMENTlink modified 2.0 years ago by Pierre Lindenbaum129k • written 2.0 years ago by aarvaBioinfo10
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