Sib-pair Command: show annotations


ClassAnalysis and data manipulation command
Nameshow 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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