Information Has Missed And Messed After Converting Annotated Whole-Genome Data Into Txt File

Question

[Tonyzeng]

Hey, I am using annovar software to annotate my variants, it works well. HOwever, when I converted annotated variant file into txt file, some of the information have missed for no reason as follows,

1) Annotation of variant file

 $ annotate_variation.pl --buildver mm10 mysnps.annovar mm10db/

OUTPUT FILE

 line57    stopgain SNV    Bclaf1:NM_001025393:exon4:c.C175T:p.R59X,Bclaf1:NM_001025392:exon4:c.C175T:p.R59X,Bclaf1:NM_153787:exon4:c.C169T:p.R57X,    chr10    20323033    20323033    C    T    chr10    20323033    .    C    T    89.96    PASS    ABHet=0.689 ;ABHom=0.985;AC=1;AF=0.500;AN=2;BaseQRankSum=0.291;DP=9;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MQ=57.04;MQ0=0;MQRankSum=-3.311;OND=0.017;QD=3.10;ReadPosRankSum=0.904    GT:AD:DP:GQ:PL    0/1:7,2:9:37:37,0,202

 line58    nonsynonymous SNV    Bclaf1:NM_001025393:exon4:c.G176A:p.R59Q,Bclaf1:NM_001025392:exon4:c.G176A:p.R59Q,Bclaf1:NM_153787:exon4:c.    =G170A:p.R57Q,    chr10    20323034    20323034    G    A    chr10    20323034    .    G    A    119.02    PASS    ABH  et=0.677;ABHom=0.985;AC=1;AF=0.500;AN=2;BaseQRankSum=1.890;DP=10;Dels=0.00;FS=1.226;HaplotypeScore=0.0000;MQ=57.08;MQ0=0;MQRankSum=-2.740;O  ND=0.017;QD=3.84;ReadPosRankSum=0.503    GT:AD:DP:GQ:PL    0/1:7,3:10:68:68,0,154

2) Convert annotated file to txt file

$ table_annovar.pl -buildver mm10 64snps.annovar.exonic_variant_function mm10db/ -protocol refGene -operation g -nastring NA

OUTPUT file (You can see easily that the orders of the each item are not corresponding to the first line as chr start end ref ....AAchange.reference, and the start/end chromosome position have missed for some reason)

Chr    Start    End    Ref    Alt    Func.refGene    Gene.refGene    ExonicFunc.refGene    AAChange.refGene

line57    stopgain    SNV    Bclaf1:NM_001025393:exon4:c.C175T:p.R59X,Bclaf1:NM_001025392:exon4:c.C175T:p.R59X,Bclaf1:NM_153787:exon4:c.
C169T:p.R57X,    chr10    NA    NA    NA    NA

line58    nonsynonymous    SNV    Bclaf1:NM_001025393:exon4:c.G176A:p.R59Q,Bclaf1:NM_001025392:exon4:c.G176A:p.R59Q,Bclaf1:NM_153787:exon4:c.    170A:p.R57Q,    chr10    NA    NA    NA    NA

line59    synonymous    SNV    Bclaf1:NM_001025393:exon4:c.G186A:p.R62R,Bclaf1:NM_001025392:exon4:c.G186A:p.R62R,Bclaf1:NM_153787:exon4:c.
G180A:p.R60R,    chr10    NA    NA    NA    NA

line60    nonsynonymous    SNV    Bclaf1:NM_001025393:exon4:c.G253A:p.G85R,Bclaf1:NM_001025392:exon4:c.G253A:p.G85R,Bclaf1:NM_153787:exon4:c.    G247A:p.G83R,    chr10    NA    NA    NA    NA

Answer 1

[Alex Paciorkowski]

I think the problem may be with your file conversion command:

$ table_annovar.pl -buildver mm10 64snps.annovar.exonic_variant_function mm10db/ -protocol refGene -operation g -nastring NA

It appears your are not asking Annovar to export all of the data columns that you want with the -protocol flag. You are getting all the .refGene columns, but you probably want more than that.

Take a look at the examples on the Annovar help page. Also, note what Annovar's developer says there:

In May 2013, I released the table_annovar.pl program to address this challenge. Since the program is new, it may have some bugs; if you encounter any, please report to me.

This may be a bug too. Try playing with other -protocol options, follow the examples first.