How to annotate vcf file using annovar?

Question

[mandecent.gupta]

I have list of thousand genome snps and I want to annotate them using annovar.

1    10177    .    A    AC    100    PASS    AC=2130;AF=0.425319;AN=5008;NS=2504;DP=103152;EAS_AF=0.3363;AMR_AF=0.3602;AFR_AF=0.4909;EUR_AF=0.4056;SAS_AF=0.4949;AA=|||unknown(NO_COVERAGE)
1    10235    .    T    TA    100    PASS    AC=6;AF=0.00119808;AN=5008;NS=2504;DP=78015;EAS_AF=0;AMR_AF=0.0014;AFR_AF=0;EUR_AF=0;SAS_AF=0.0051;AA=|||unknown(NO_COVERAGE)
1    10352    rs145072688    T    TA    100    PASS    AC=2191;AF=0.4375;AN=5008;NS=2504;DP=88915;EAS_AF=0.4306;AMR_AF=0.4107;AFR_AF=0.4788;EUR_AF=0.4264;SAS_AF=0.4192;AA=|||unknown(NO_COVERAGE)

Command

perl annotate_variation.pl -buildver hg19 ../1000G_records_sorted.vcf.filtINS.filtCN humandb/

But it generates one 1000G_records_sorted.vcf.filtINS.filtCN.invalid_input file which has all the records and no output in .variant_function and .exonic_variant_function file.

It seems above parameter are not sufficient for processing vcf file. Pls suggest how can I annotate vcf file?

[Pierre Lindenbaum]

Hello mandecent.gupta!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=50323

This is typically not recommended as it runs the risk of annoying people in both communities.

[mandecent.gupta]

Ok, thanks for advise.