Invalid alternative alleles in ANNOVAR

Question

[bisansamara]

I have a text file with genetic variants, and I need to annotate them using ANNOVAR. I first have to convert the input file into ANNOVAR accepted format (vcf4). So when I run the following command:

perl convert2annovar.pl test.txt -format vcf4 -allsample -withfreq > test.vcf4

I get this error: WARNING: 7 invalid alternative alleles found in input file and all the the 'alt' nucleotides in the resulting vcf4 file became '0'.

Any suggestions on what does that mean, and how to fix it? I need the 'alt' nucleotides to be in my output file.

Files in input txt file are:

chr start end ref alt col6 col7 col8
7   127991051   127991052   G   A   22542183    1   32
18  321719  321720  C   A   22542183    1   32
5   76174153    76174154    G   T   22542183    1   32
9   129829544   129829545   T   C   22542183    1   32
9   127682438   127682438   C   -   25621899    1   32
1   1954912 1954913 C   T   22542183    1   32
8   27505096    27505097    C   T   22542183    1   32

Answer 1

[Kevin Blighe]

The problem appears to be that you are supplying a TXT file as input to a function that expects VCF due to the -format vcf4 command line parameter that you're passing.

Please review the accepted ANNOVAR input formats / conversions here: ANNOVAR input file.

Kevin