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| To view a specific region of records (such as APOL1 g2 allele) | | To view a specific region of records (such as APOL1 g2 allele) |
| | | |
− | ${GC}/bin/tabix ${OUT}/final/all.genotypes.vcf.gz 22:36662041-36662041 | + | ${GC}/bin/tabix ${OUT}/indel/final/all.genotypes.vcf.gz 22:36662041-36662041 |
| | | |
| The columns are CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, Genotype fields denoted by the sample name. | | The columns are CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, Genotype fields denoted by the sample name. |
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| HWE_LLR=-0.0222464;HWE_LPVAL=-0.182794;HWE_DF=1; | | HWE_LLR=-0.0222464;HWE_LPVAL=-0.182794;HWE_DF=1; |
| FIC=-0.00372601;AB=0.384578 | | FIC=-0.00372601;AB=0.384578 |
− | GT:PL:DP:AD:GQ 0/0:0,9,158:3:3,0,0:10 0/0:0,18,281:6:6,0,0:18 | + | GT:PL:DP:AD:GQ 0/0:0,6,145:3:2,0,1:7 0/0:0,12,192:4:4,0,0:12 |
| | | |
| Here is a description of the record's fields. | | Here is a description of the record's fields. |
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| INFO : fields containing information about the variant. | | INFO : fields containing information about the variant. |
| FORMAT : format field labels for the genotype columns. | | FORMAT : format field labels for the genotype columns. |
− | 0/0:0,9,158:3:3,0,0:10 : genotype information. | + | 0/0:0,6,145:3:2,0,1:7 : genotype information. |
| | | |
| 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}/final/all.genotypes.vcf.gz | + | ${GC}/bin/vt view -i 22:36990878-36990879 ${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 |