VCF to ANNOVAR format

Question

[reza.jabal]

Here, I've got a VCF file I want to convert to ANNOVAR format through running the following command, but apparently it is not working!

table_annovar.pl 1_23_intersect.vcf /scratch/GENE_DATABASES/humandb/HG19_APR13/ -protocol refGene,phastConsElements44way,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp135,ljb_all -operation g,r,r,f,f,f,f -vcfinput .

I was wondering if anyone has any suggestion on how to sort this out.

[Samar]

Could you solve the issue? Even I am facing the same problem. Everytime I use this table_annovar.pl, I get an error, saying its a syntax issue.

[Karma]

./convert2annovar.pl -format vcf4 input.vcf > output.vcf

Answer 1

[ebrown1955]

The -vcfinput option is relatively new, and if it's not working then you might have an older version of Annovar. Try updating to the most current release.

If all else fails, use convert2annovar.pl, i.e.

convert2annovar.pl -format vcf4 1_23_intersect.vcf > 1_23_intersect.annovar

Then you can use table annovar in some variant of this:

table_annovar.pl 1_23_intersect.annovar /scratch/GENE_DATABASES/humandb/HG19_APR13/ -protocol refGene,phastConsElements44way,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp135,ljb_all -operation g,r,r,f,f,f,f -csvout .

Answer 2

[cpad0112]

Download the converter from here.

Try running simple command like this on your vcf file:

perl convert2annovar.pl -format vcf4 ex2.vcf

You can download ex2.vcf from here.

This perl script seems to be working and output I got was:

WARNING to old ANNOVAR users: this program no longer does line-to-line conversion for multi-sample VCF files. If you want to include all variants in output, use '-format vcf4old' or use '-format vcf4 -allsample -withfreq' instead.
20    1110696    1110696    A    G    het    67    6
20    1110696    1110696    A    T    het    67    6
20    1234568    1234569    TC    -    het    50    4
NOTICE: Finished reading 27 lines from VCF file
NOTICE: A total of 5 locus in VCF file passed QC threshold, representing 5 SNPs (2 transitions and 2 transversions) and 2 indels/substitutions
NOTICE: Finished writing 2 SNP genotypes (1 transitions and 1 transversions) and 1 indels/substitutions for 1 sample (but input contains 3 samples)
WARNING: 1 invalid alternative alleles found in input file

Run your VCF file through VCF validating tools. Upgrade/update perl script tool as mentioned above. First try running with simple commands.