Question: How to get strand-specific nucleotide change annotation in ANNOVAR?
1
gravatar for bounlu
3.4 years ago by
bounlu180
Singapore
bounlu180 wrote:

In the ANNOVAR output, there is annotation for the nucleotide change only for the coding variants (exonic, splicing, UTRs etc.) but not for intronic variants. How to get the actual nucleotide change on the transcript in a strand-specific manner for all input variants?

In the example output below, genes ATM and CLPX both have a change of A>G although the input Ref & Alt are A>G and T>C, respectively. How can I get the same info for intronic variants as well?

Chr Start   End Ref Alt Func.refGene    Gene.refGene    GeneDetail.refGene
8   42388940    42388940    T   C   intronic    SLC20A2 -
1   207943260   207943260   A   G   intronic    CD46    -
16  74361884    74361884    T   C   intergenic  PSMD7,LOC283922 dist=21698;dist=4420
10  44067194    44067194    T   C   intronic    ZNF239  -
16  89582444    89582444    A   G   intronic    SPG7    -
1   155696455   155696455   A   G   intronic    DAP3    -
4   140520751   140520751   T   C   intergenic  SETD7,MGST2 dist=42828;dist=66171
16  89755457    89755457    A   G   intronic    CDK10   -
11  108236477   108236477   A   G   UTR3    ATM NM_000051:c.*242A>G
12  42753813    42753813    A   G   intronic    PPHLN1  -
16  592643  592643  A   G   intronic    CAPN15  -
11  493435  493435  A   G   intergenic  PTDSS2,RNH1 dist=2048;dist=1077
20  34218094    34218094    T   C   intronic    CPNE1   -
19  44663518    44663518    A   G   UTR3    ZNF234  NM_006630:c.*1246A>G,NM_001144824:c.*1246A>G
15  65442032    65442032    T   C   UTR3    CLPX    NM_006660:c.*1129A>G
1   6283439 6283439 T   C   UTR3    ICMT    NM_012405:c.*1701A>G
18  12031309    12031309    A   G   downstream  IMPA2   -
X   48342958    48342958    A   G   intronic    FTSJ1   -
2   178161752   178161752   A   G   ncRNA_intronic  LOC100130691    -
annovar • 1.1k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by bounlu180
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