Dear samtools developer,
I doing SNP/Indel detection of multiple bam files with mpileup.
I was using the version 0.19 and it was ok.I updated the version to 1.2 and I
have some doubts about GT values of my samples.
For some samples I had GT value = "./.:0,0,0".
I think this means missing value.
But for the same sample and command line in the previous version, I had for the
same sample the GT = 0/0 or 0/1 (and no ./.)
I checked some SNPs with tview and the results with the previous version make
sense. So what is happening?
Why I had so many GT = ./. ?? I had plenty of reads.
Example of result with version 1.2
Chr10 517 . G A 33.6435 .
DP=10;VDB=0.588406;SGB=-0.178207;RPB=0.274945;MQB=0.733186;MQSB=0.727822;BQB=0
.916482;MQ0F=0;ICB=0.219101;HOB=0.0703125;AC=3;AN=16;DP4=6,1,0,3;MQ=30 GT:PL
./.:0,0,0 0/0:0,6,63 ./.:0,0,0 ./.:0,
0,0 ./.:0,0,0 0/1:21,3,0 ./.:0,0,0 0/0:0,3,31
./.:0,0,0 0/1:40,3,0 0/0:0,3,31 0/0:0,6,57 0/0:0,3,31
0/1:21,3,0
Chr10 617 . G A 17.3233 .
DP=41;VDB=0.42;SGB=-2.81556;RPB=0.9;MQB=0.557143;MQSB=0.0813562;BQB=0.971429;M
Q0F=0;ICB=0.0275862;HOB=0.0118343;AC=2;AN=26;DP4=26,9,1,1;MQ=34 GT:PL
0/0:0,9,102 0/0:0,15,106 0/1:30,0,26 0/0:0,9,97 0/0:0,9,104
0/0:0,9,89 0/0:0,12,100 0/0:0,3,28 0/0:0,12,116 0/0:0,12,97
0/1:34,0,25 0/0:0,6,63 0/0:0,
3,31 ./.:0,0,0
Any suggestions?
thanksClarissa Boschiero
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