samtools mpileup - different results for versions 0.19 x 1.1

[clarissaboschi]

Dear Members

I ran the same parameters and files with samtools/mpileup version 0.19 x 1.1.

I had different number of SNPs, quality, etc, but the result that I am worried is the GT (genotype) of my samples.

I have 14 samples, and I did not understand why in the new version I had many samples with the GT = "./.", but in the previous version is "0/0" (the sample is homozygous reference).

I think "./." means missing allele? Why is it happening?

Example of my results for the same SNP

version 0.19
Chr10 414 . C T 70.3 . DP=14;VDB=7.635114e-02;RPB=-1.060660e+00;AF1=0.2769;AC1=8;DP4=1,9,0,4;MQ=38;FQ
=71.7;PV4=1,0.27,1,1 GT:PL:GQ 0/0:0,0,0:3 0/0:0,3,31:6 0/1:31,0,22:27 0/0:0,0,0:3 0/1:59,0,28:35 0/0:0,0,0:3 -0/1:28,0,59:27 0/0:0,6,67:8 0/0:0,0,0:3 0/0:0,0,0:3 0/0:0,0,0:3 0/0:0,3,33:6 0/0:0,6,64:8 0/0:0,0,0:3

version 1.1
Chr10 414 . C T 75 PASS DP=14;VDB=0.0665622;SGB=-0.0571639;RPB=0.485537;MQB=0.236928;MQSB=1;BQB=0.9607
89;MQ0F=0;ICB=0.304615;HOB=0.0918367;AC=3;AN=14;DP4=1,9,0,4;MQ=38 GT:PL ./.:0,0,0 0/0:0,3,31 0/1:31,0,22 ./.:0,0,0 0/1:59,0,28 ./.:0,0,0 0/1:28,0,59 0/0:0,6,67 ./.:0,0,0 ./.:0,0,0 ./.:0,0,0 0/0:0,3,33 0/0:0,6,64 ./.:0,0,0

I also checked some of those SNPs with tview. Some of the SNPs with ./. genotype I can see only the alternate allele for all reads or sometimes only the reference allele. There are plenty of reads for one specific SNP.

Any suggestion?
Thanks