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| | | |
| 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 |
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| 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===== |
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| | | |
| 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 |
− | 3,0,0 : allele depth | + | 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. |
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| 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. |
− | 10 : genotype quality | + | 7 : genotype quality |
| | | |
| == INDEL Analysis == | | == INDEL Analysis == |