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



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



