ANNOVAR annotate frameshift

Question

[sugus]

Hi there, I met a problem when annotate a nonframshift substitution but it was supposed to be frameshilt. Here is the example of data (test.avinput) and code.

my data and the confusing annotations are the last two which I thought they were supposed to be frameshift.

14 69256505 69256505 G A
14 69256506 69256506 G A
14 69256987 69256987 C -
14 69257040 69257041 -- GG
14 69257144 69257145 -- CC

my cmd: annotate_variation.pl -out test -build hg19 example/test.avinput humandb/

After annotation I got the following results and I do not know why the last two are nonframshift.

line1 synonymous SNV ZFP36L1:NM_004926:exon2:c.C762T:p.S254S,ZFP36L1:NM_001244698:exon2:c.C762T:p.S254S,ZFP36L1:NM_001244701:exon3:c.C969T:p.S323S, 14 69256505 69256505 G A
line2 nonsynonymous SNV ZFP36L1:NM_004926:exon2:c.C761T:p.S254F,ZFP36L1:NM_001244698:exon2:c.C761T:p.S254F,ZFP36L1:NM_001244701:exon3:c.C968T:p.S323F, 14 69256506 69256506 G A
line3 frameshift deletion ZFP36L1:NM_004926:exon2:c.280delG:p.G94fs,ZFP36L1:NM_001244698:exon2:c.280delG:p.G94fs,ZFP36L1:NM_001244701:exon3:c.487delG:p.G163fs, 14 69256987 69256987 C -
line4 nonframeshift substitution ZFP36L1:NM_004926:exon2:c.226_227CC,ZFP36L1:NM_001244698:exon2:c.226_227CC,ZFP36L1:NM_001244701:exon3:c.433_434CC, 14 69257040 69257041 -- GG
line5 nonframeshift substitution ZFP36L1:NM_004926:exon2:c.122_123GG,ZFP36L1:NM_001244698:exon2:c.122_123GG,ZFP36L1:NM_001244701:exon3:c.329_330GG, 14 69257144 69257145 -- CC

Many thanks advanced!

[Kevin Blighe]

They are non-frame-shift because your encoding indicates that 2 bases are being substituted by 2 bases; thus, there is no frame-shift.

Your encoding is the same as saying:

14 69256505 69256505 G A
14 69256506 69256506 G A
14 69256987 69256987 C -
14 69257040 69257041 GC GG
14 69257144 69257145 CA CC

GC and CA are the bases in hg19 / GRCh37.

Kevin

[sugus]

Thank you for pointing this out but actually what's wrong is my input format. I have solved this problem and attached the solution below.

Thanks again, Kevin.

Answer 1

[sugus]

I have solved this problem actually my input data format for ANNOVAR is wrong.

For those two insertion, it should change the end postion and the "-" to the following:

14 69257040 69257040 - GG
14 69257144 69257144 - CC

and if the mutation is a deletion, the end postion should correspond to bp length but still only one "-".

Basically,

#if the mutation is a kind of insertion : the start should be equal to end, and AlleleA should only be one -
#if the mutation is a kind of deletion : the end should consider bp length and AlleleB should only be one -

Thanks.