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Revision as of 18:12, 15 June 2014
, 18:12, 15 June 2014→Tools
This wiki page details some standard Indel analyses which hopefully can help the group in understanding the issues and perform the analyses quickly without reinventing the wheel.
This wiki page details some standard Indel analyses which hopefully can help the group in understanding the issues and perform the analyses quickly without reinventing the wheel.
== Anatomy of all.genotypes.bcf ==
You can access the header by running the command:
vt view -H all.genotypes.bcf.
The header is as follows:
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=22,length=51304566>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
##FORMAT=<ID=AD,Number=3,Type=Integer,Description="Allele Depth">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Alternate Allele Counts">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Number Allele Counts">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=AF,Number=A,Type=Float,Description="Alternate Allele Frequency">
##INFO=<ID=GC,Number=G,Type=Integer,Description="Genotype Counts">
##INFO=<ID=GN,Number=1,Type=Integer,Description="Total Number of Genotypes Counts">
##INFO=<ID=GF,Number=G,Type=Float,Description="Genotype Frequency">
##INFO=<ID=HWEAF,Number=A,Type=Float,Description="Genotype likelihood based MLE Allele Frequency assuming HWE">
##INFO=<ID=HWEGF,Number=G,Type=Float,Description="Genotype likelihood based MLE Genotype Frequency assuming HWE">
##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Genotype likelihood based MLE Allele Frequency">
##INFO=<ID=MLEGF,Number=G,Type=Float,Description="Genotype likelihood based MLE Genotype Frequency">
##INFO=<ID=HWE_LLR,Number=1,Type=Float,Description="Genotype likelihood based Hardy Weinberg ln(Likelihood Ratio)">
##INFO=<ID=HWE_LPVAL,Number=1,Type=Float,Description="Genotype likelihood based Hardy Weinberg Likelihood Ratio Test Statistic ln(p-value)">
##INFO=<ID=HWE_DF,Number=1,Type=Integer,Description="Degrees of freedom for Genotype likelihood based Hardy Weinberg Likelihood Ratio Test Statistic">
##INFO=<ID=FIC,Number=1,Type=Float,Description="Genotype likelihood based Inbreeding Coefficient">
##INFO=<ID=AB,Number=1,Type=Float,Description="Genotype likelihood based Allele Balance">
##FILTER=<ID=TPASS,Description="Temporary pass">
##FILTER=<ID=overlap,Description="Overlapping variant">
=== body ===
To view some of the records:
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;
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
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 GT:PL:DP:AD:GQ 0/0:0,12,155:6:4,0,2:12
22 36995311 . GA G . TPASS AC=61;AN=124;AF=0.491935;GC=21,21,20;GN=62;GF=0.33871,0.33871,0.322581;NS=62;HWEAF=0.492227;HWEGF=0.257834,0.499879,0.242287;MLEAF=0.492028;MLEGF=0.298019,0.419905,0.282076;HWE_LLR=-0.605122;HWE_LPVAL=-1.30459;HWE_DF=1;FIC=0.0444598;AB=0.53981 GT:PL:DP:AD:GQ 0/1:55,0,24:3:1,2,0:24
22 36995329 . GA G . TPASS AC=2;AN=124;AF=0.016129;GC=60,2,0;GN=62;GF=0.967742,0.0322581,0;NS=62;HWEAF=0.0164696;HWEGF=0.967332,0.0323966,0.000271246;MLEAF=0.0165148;MLEGF=0.96697,0.0330296,7.28675e-44;HWE_LLR=-0.0171385;HWE_LPVAL=-0.158856;HWE_DF=1;FIC=-0.00275028;AB=0.339746 GT:PL:DP:AD:GQ 0/0:0,9,97:5:3,0,2:10
=Tools=
=Tools=
