ANNOVAR is not reading input data

Question

[Maryam]

Hello every one

I don't have vcf file to I am pasting my variants in ANNOVAR. I created my variant format based on sample file given on website.

The software is successfully reading the sample file both as input window and TXT file. But when I paste my data in same format, ANNOVAR is not reading it.

Can someone please help

This my my example data:

10  61901713    63661472    G   C
14  104780214   105246551   C   T
16  2175613 2225614 G   T

This is example data from website:

7   92570705    92570705    T   C
7   98870495    98870495    G   A
7   99835402    99835402    C   T

[Ram]

Are you using a web version of annovar? If so, can you show us the link, please?

Also, don't use phrases like "need urgent help" - this is a forum where people contribute when they have time, so your urgency can't really be factored in.

[Maryam]

Apologies for the phrase this is the link: https://wannovar.wglab.org/

[Ram]

Where did you get the example data from? I can't find it on the website.

[Maryam]

hello I got the data from here https://annovar.openbioinformatics.org/en/latest/user-guide/input/

[Ram]

I pasted the first three lines from the avinput file and while I don't see any output in the exome files (probably no exonic variants), I see genome output. Make sure that when you paste, you pick the right format. For the example from the ANNOVAR website (the avinput file, the right format is "ANNOVAR", not "VCF"). Try ANNOVAR as input format for your minimal input (just the CHR, START, STOP, REF, ALT that you're using) and see if that works.