Hi - can you send the two command lines you used for 0.1.19 and 1.2?
Rgds, Thomas On 10/02/15 10:19, Clarissa Boschiero wrote:
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? thanks Clarissa Boschiero ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
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------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/
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