Question: Invalid alternative alleles in ANNOVAR
gravatar for bisansamara
2.6 years ago by
bisansamara10 wrote:

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 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

annotation allel error annovar • 1.3k views
ADD COMMENTlink modified 2.6 years ago by Kevin Blighe69k • written 2.6 years ago by bisansamara10
gravatar for Kevin Blighe
2.6 years ago by
Kevin Blighe69k
Republic of Ireland
Kevin Blighe69k wrote:

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.


ADD COMMENTlink written 2.6 years ago by Kevin Blighe69k
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