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Revision as of 01:16, 6 December 2014
, 01:16, 6 December 2014→Records
You can obtain the same output by using the following command
You can obtain the same output by using the following command
${GC}/bin/vt view -i 22:36990878-36990879 ${OUT}/indel/final/all.genotypes.vcf.gz
${GC}/bin/vt view -i 22:36662041-36662041 ${OUT}/indel/final/all.genotypes.vcf.gz
* -i specifies the region
* -i specifies the region
* You can leave it out and look at all the records
* You can leave it out and look at all the records
AF=0.017 : allele frequency based on AC/AN
AF=0.017 : allele frequency based on AC/AN
GC=55,2,0 : genotype counts for 0/0, 0/1, 1/1
GC=55,2,0 : genotype counts for 0/0, 0/1, 1/1
GF=0.55,0.34,0.10 : genotype frequencies based on GC
GF=0.96,0.04,0 : genotype frequencies based on GC
NS=57 : no. of samples
NS=57 : no. of samples
HWEAF=0.28 : genotype likelihood based estimation of the allele frequency assuming Hardy Weinberg equilibrium
HWEAF=0.020 : genotype likelihood based estimation of the allele frequency assuming Hardy Weinberg equilibrium
HWEGF=0.52,0.40,0.08 : genotype frequency derived from HWEAF
HWEGF=0.96,0.04,0.00 : genotype frequency derived from HWEAF
HWE_LPVAL=-1.08 : log p value of HWE test
HWE_LPVAL=-0.18 : log p value of HWE test
FIC=-0.07 : genotype likelihood based inbreeding coefficient
FIC=-0.003 : genotype likelihood based inbreeding coefficient
AB=0.61 : genotype likelihood based allele balance
AB=0.38 : genotype likelihood based allele balance
=====GENOTYPE field=====
=====GENOTYPE field=====
0/0 : homozygous reference chosen based on PL
0/0 : homozygous reference chosen based on PL
0,9,158 : PHRED scaled genotype likelihoods
0,6,145 : PHRED scaled genotype likelihoods
3 : no. of reads covering this variant
3 : no. of reads covering this variant
2,0,1 : allele depth
counts of reads supporting the reference allele,
counts of reads supporting the reference allele,
the alternative allele and neither alleles respectively.
the alternative allele and neither alleles respectively.
coverage of the read over the locus
coverage of the read over the locus
or simply an allele that is not accounted for.
or simply an allele that is not accounted for.
7 : genotype quality
== INDEL Analysis ==
== INDEL Analysis ==
