Hi,

I ran VARSCAN2 mpileup2snp to call SNPs and generated a vcf file.

However, I noticed a strange thing about the NC flag. This is apparently INFO=<id=nc,number=1,type=integer,description="number of="" samples="" not="" called"="">

However, I see

TR43100|c0_g1_i1    792 .   T   C   .   PASS    ADP=0;WT=1;HET=0;HOM=1;NC=17    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    ./.:.:0 ./.:.:0 ./.:.:0 ./.:.:1 ./.:.:0 ./.:.:1 ./.:.:0 ./.:.:0 ./.:.:1 0/0:10:5:5:5:0:0%:1E0:38:0:0:5:0:0  ./.:.:0 ./.:.:1 ./.:.:1 1/1:7:2:2:0:2:100%:1.6667E-1:0:33:0:0:1:1   ./:.:0  ./:.:0  ./:.:0  ./:.:0  ./:.:0

This has NC=17 and I can see from the 19 samples 2 have been called. This seems correct.

TR43100|c1_g1_i1    351 .   T   C   .   PASS    ADP=0;WT=1;HET=1;HOM=0;NC=17    GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR    ./:.:0  ./:.:0  ./:.:0  ./:.:0  ./:.:0  ./:.:1  ./:.:0  ./:.:0  ./:.:0  ./:.:2  ./:.:0  ./:.:0  ./:.:0  0/1:6:4:4:2:2:50%:2.1429E-1:40:38:2:0:1:1   ./:.:0  ./:.:0  ./:.:0  ./:.:0  ./:.:0

This has NC=17 abut I can only see one sample that has been called? What have I missed, why isn't NC=18 here?

And it says WT=1. Where is the WT? This should be 0/0

And also TR43100|c0_g1_i1 763 . G A . PASS ADP=0;WT=2;HET=0;HOM=1;NC=16 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR ./.:.:0 ./.:.:0 ./.:.:0 1/1:13:3:3:0:3:100%:5E-2:0:39:0:0:0:3 ./.:.:0 ./.:.:1 ./.:.:0 ./.:.:0 ./.:.:1 0/0:6:3:3:3:0:0%:1E0:40:0:0:3:0:0 ./.:.:0 ./.:.:1 ./.:.:1 ./.:.:2 ./.:.:0 ./.:.:0 ./.:.:0 ./.:.:0 ./.:.:0

Where are the 2 WT? I can only see 1 0/0