1,102
edits
Changes
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Revision as of 20:07, 15 June 2014
, 20:07, 15 June 2014→Records
vt view all.genotypes.bcf.
vt view all.genotypes.bcf.
22 36990877 . GGT G . TPASS AC=32;AN=116;AF=0.275862;GC=32,20,6;GN=58;GF=0.551724,0.344828,0.103448;NS=58;
The columns are CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, Genotype fields denoted by the sample name.
MLEGF=0.494275,0.464129,0.0415952;HWE_LLR=-0.453098;HWE_LPVAL=-1.0755;HWE_DF=1;FIC=-0.0718807;AB=0.6129
22 36990877 . GGT G . TPASS AC=32;AN=116;AF=0.275862;GC=32,20,6;GN=58;
GF=0.551724,0.344828,0.103448;NS=58;
22 36991203 . TGAG T . TPASS AC=5;AN=124;AF=0.0403226;GC=58,3,1;GN=62;GF=0.935484,0.0483871,0.016129;NS=62;HWEAF=0.0355594;HWEGF=0.930145,0.0685899,0.00126447;MLEAF=0.0353706;MLEGF=0.929259,0.0707412,5.94815e-11;HWE_LLR=-0.0443401;HWE_LPVAL=-0.266754;HWE_DF=1;FIC=-0.0109029;AB=0.562243
HWEAF=0.275797;HWEGF=0.52447,0.399466,0.0760642;
MLEAF=0.27366; MLEGF=0.494275,0.464129,0.0415952;
HWE_LLR=-0.453098;HWE_LPVAL=-1.0755;HWE_DF=1;
FIC=-0.0718807;AB=0.6129
GT:PL:DP:AD:GQ 0/0:0,9,108:9:3,0,6:10
Let's look at the first 5 records.
22 : chromosome
36990877 : genome position
. : this is the ID field that is left blank.
GGT : the reference sequence that is replaced by the alternative sequence below.
G : so this is basically a deletion of GT
. : QUAL field which is left missing.
TPASS : a temporary passed variant.
INFO : fields containing information about the variant.
FORMAT : format field labels for the genotype columns.
0/0:0,9,108:9:3,0,6:10 : genotype information.
=Tools=
=Tools=
