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GenotypeGVCFs -allSites

blueskypyblueskypy Member ✭✭
edited October 2014 in Ask the GATK team

Could you help me with the output? Here are some output:

##INFO=<ID=NCC,Number=1,Type=Integer,Description="Number of no-called samples">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  s1      s5
21      1       .       N       .       .       .       NCC=2   GT:DP   0/0:0   0/0:0
21      2       .       N       .       .       .       NCC=2   GT:DP   0/0:0   0/0:0
21      3       .       N       .       .       .       NCC=2   GT:DP   0/0:0   0/0:0
21      4       .       N       .       .       .       NCC=2   GT:DP   0/0:0   0/0:0
Some lines from chr1
1       11381   .       T       .       .       .       NCC=2   GT:DP   0/0:0   0/0:0
1       11382   .       T       .       .       .       NCC=2   GT:DP   0/0:0   0/0:0
1       13812   .       C       .       .       .       DP=2;NCC=2      GT:DP   0/0:0   0/0:2
1       13813   .       T       .       .       .       DP=2;NCC=2      GT:DP   0/0:0   0/0:2
1       14930   .       A       G       109.67  .      AC=2;AF=0.500;AN=4;DP=8;FS=0.000;GQ_MEAN=7.50;GQ_STDDEV=10.61;MLEAC=3;MLEAF=0.750;MQ=36.44;MQ0=0;NCC=0;QD=21.93   GT:AD:DP:GQ:PL  1/1:0,5:5:15:138,15,0   0/0:3,0:3:0:0,0,42

Questions:

  1. Why GT 0/0 instead of ./. when DP is 0?

  2. On NCC, what is “no-called samples”? Should it be NNC (Number of No Called)?

Best Answer

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