| 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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