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edits
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Revision as of 01:10, 6 December 2014
, 01:10, 6 December 2014→Records
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.
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.
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
