Class | Analysis and data manipulation command |
Name | show annotations |
Arguments | <VCF_file> [locus|position|alleles|<INFO_var1>[...<INFO_varN>]]. |
Crosstabulate values of INFO variables in a VCF file. Variables that contain subvariables can be accessed using the form <Variable_name>:<Subvariable_name>.
Example:
>> show ann topHRC.sites.vcf.gz "AC": Alternate allele count in called genotypes "AN": Total number of alleles in called genotypes "AF": Alternate allele frequency from called genotypes "AC_EXCLUDING_1000G": Alternate allele count in called genotypes excluding 1000G samples "AN_EXCLUDING_1000G": Total number of alleles in called genotypes excluding 1000G samples "AF_EXCLUDING_1000G": Alternate allele frequency from called genotypes excluding 1000G samples "AA": Ancestral allele No. INFO vars = 7 >> show ann topHRC.sites.vcf.gz AA *FOUND* "AA": Ancestral allele No. INFO vars = 7 index AA Frequency ------- -- ---------- 1: . 768 (0.808) 2: - 105 (0.111) 3: A 12 (0.013) 4: C 21 (0.022) 5: G 26 (0.027) 6: T 18 (0.019) ---------- Total 950 >> sho ann gnomad_KITLG-TPCN2-PAH-POMC-SLC24A4.vcf CSQ:SYMBOL CSQ:IMPACT *FOUND* "CSQ:IMPACT" (3) *FOUND* "CSQ:SYMBOL" (4) No. INFO vars = 174 (68 subvars) index CSQ:4 CSQ:3 Frequency ------- ------- -------- ---------- 1: KITLG HIGH 11 (0.003) 2: KITLG LOW 61 (0.018) 3: KITLG MODERATE 116 (0.033) 4: KITLG MODIFIER 226 (0.065) 5: PAH HIGH 37 (0.011) 6: PAH LOW 130 (0.037) 7: PAH MODERATE 239 (0.069) 8: PAH MODIFIER 264 (0.076) 9: POMC HIGH 20 (0.006) 10: POMC LOW 86 (0.025) 11: POMC MODERATE 214 (0.062) 12: POMC MODIFIER 31 (0.009) 13: SLC24A4 HIGH 30 (0.009) 14: SLC24A4 LOW 180 (0.052) 15: SLC24A4 MODERATE 292 (0.084) 16: SLC24A4 MODIFIER 335 (0.097) 17: TPCN2 HIGH 46 (0.013) 18: TPCN2 LOW 281 (0.081) 19: TPCN2 MODERATE 379 (0.109) 20: TPCN2 MODIFIER 491 (0.142) ---------- Total 3469
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