ANNOVAR precedence of annotation/specific transcript

Question

[gero.knittel]

Hi everybody,

I have a list of recurrent mutations from a WGS dataset. I would like to know on which exons they sit (the exon number for a certain transcript).

If there are multiple transcripts at a certain position, annovar puts out a list with all nonsynonymous SNVs and I can just pick the transcript I want. My only problem is the following: If there is for example a stoploss for any of the transcripts at that genomic position, ANNOVAR doesn't output the nonsynonymous SNVs anymore, but only a list of mutation of that category, which has a higher precedence.

Is there any way to change that? Can I either change the precedence, or tell the software to output the effects on all transcripts or anything similar?

Best regards, and thanks a lot in advance, Gero

[Kevin Blighe]

It should output all overlapping genes and all consequences. Can you paste the record in question / paste an example?

Which version of the genome are you using.

[gero.knittel]

Hi Kevin,

Thanks for the reply!

This is the example input file (or a selection of it):

3   38182727    38182727    A   C   0.0 0.0061  0.0087  0.0035  MYD88   4615
3   38182316    38182316    A   G   0.0034  0.0 0.0 0.0017  MYD88   4615
3   38182641    38182641    T   C   0.2881  0.0122  0.0783  0.1672  MYD88   4615

This is the exonic variant output file for the three lines above:

line17  nonsynonymous SNV   MYD88:NM_002468:exon5:c.A880C:p.T294P,MYD88:NM_001172568:exon4:c.A745C:p.T249P,MYD88:NM_001172567:exon5:c.A904C:p.T302P,    3   38182727    38182727    A   C   0.0 0.0061  0.0087  0.0035  MYD88   4615
line18  nonsynonymous SNV   MYD88:NM_002468:exon4:c.A752G:p.K251R,MYD88:NM_001172569:exon3:c.A571G:p.N191D,MYD88:NM_001172568:exon3:c.A617G:p.K206R,MYD88:NM_001172566:exon2:c.A436G:p.N146D,MYD88:NM_001172567:exon4:c.A776G:p.K259R,  3   38182316    38182316    A   G   0.0034  0.0 0.0 0.0017  MYD88   4615
line19  stoploss    MYD88:NM_001172569:exon4:c.T613C:p.X205R,MYD88:NM_001172566:exon3:c.T478C:p.X160R,  3   38182641    38182641    T   C   0.2881  0.0122  0.0783  0.1672  MYD88   4615

Unfortunately, for line 19, the effect on transcript NM_002468 is not given. But NM_002468 is present at position 3:3812641 and the mutation should cause a p.L265P mutation on that transcript, if I check on the UCSC genome browser on hg19, which is the genome version I'm using.

I really hope you can help me out. Let me know if you need anything additional info.

Best, Gero

[Kevin Blighe]

Thanks, I will have to check when I get home later today.

[Kevin Blighe]

I have posted an answer for you.

Answer 1

[Kevin Blighe]

Hello, all that you need to add is the --separate command line parameter:

1, view input:

cat test.ann
3   38182727    38182727    A   C
3   38182316    38182316    A   G
3   38182641    38182641    T   C

2, annotate:

perl annotate_variation.pl -out ex1 -build hg19 test.ann /Programs/annovar/humandb/ --separate

3, view output:

cat ex1.exonic_variant_function

line1   nonsynonymous SNV   MYD88:NM_001172568:exon4:c.A745C:p.T249P,MYD88:NM_002468:exon5:c.A880C:p.T294P,MYD88:NM_001172567:exon5:c.A904C:p.T302P,    3   38182727    38182727    A   C
line2   nonsynonymous SNV   MYD88:NM_001172568:exon3:c.A617G:p.K206R,MYD88:NM_001172569:exon3:c.A571G:p.N191D,MYD88:NM_002468:exon4:c.A752G:p.K251R,MYD88:NM_001172566:exon2:c.A436G:p.N146D,MYD88:NM_001172567:exon4:c.A776G:p.K259R,  3   38182316    38182316    A   G
line3   stoploss    MYD88:NM_001172569:exon4:c.T613C:p.X205R,MYD88:NM_001172566:exon3:c.T478C:p.X160R,  3   38182641    38182641    TC
line3   nonsynonymous SNV   MYD88:NM_001172568:exon4:c.T659C:p.L220P,MYD88:NM_002468:exon5:c.T794C:p.L265P,MYD88:NM_001172567:exon5:c.T818C:p.L273P,    3   38182641    38182641    T   C

[gero.knittel]

Thank you very much!!

Great, have a good weekend!

[Kevin Blighe]

Not sure, I invariably work 7 days per week. That's the way that it is these days.

Catch you later!