i-stats plinkseq

[mcri...@gmail.com]

Hello everybody
I'm a new user of Plinkseq and I am trying to analyze a compressed vcf with around 400 samples of WES (I'm a beginner!). I am having some questions and troubles regarding the i-stats function. When I executed  i-stats on the compressed vcf I obtained some samples that lacked some column values as PASS_S or PASS resulting on a movement of values and the assignment of incorrect values for these samples on some columns. I observed that SING column contain the same values that PASS_S and NMIN contain the same values that PASS for mostly all the samples but still some of them lost PASS or PASS_S values.  Moreover, when I tried to perform i-stats on the individual vcf for some of these samples the values obtained are close but different and the ouput contain values on those reported as missed on the overall analysis. I would appreciate if someone could help me with this issue and/or told me what could be happen. My main concern is if it could be due to some problem with the compressed vcf.
Thank you very much in advance!
Best regards
Cristina