Question: VCF to ANNOVAR format
gravatar for reza.jabal
4.8 years ago by
New York, USA
reza.jabal420 wrote:

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! 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.

next-gen software error • 4.5k views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 4.8 years ago by reza.jabal420

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

ADD REPLYlink modified 8 months ago by RamRS28k • written 4.8 years ago by Samar0
./ -format vcf4 input.vcf > output.vcf
ADD REPLYlink written 2.9 years ago by Karma270
gravatar for ebrown1955
4.8 years ago by
United States
ebrown1955300 wrote:

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, i.e. -format vcf4 1_23_intersect.vcf > 1_23_intersect.annovar

Then you can use table annovar in some variant of this: 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 .
ADD COMMENTlink modified 8 months ago by RamRS28k • written 4.8 years ago by ebrown1955300
gravatar for cpad0112
4.8 years ago by
cpad011213k wrote:

Download the converter from here.

Try running simple command like this on your vcf file:

perl -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.

ADD COMMENTlink modified 8 months ago by RamRS28k • written 4.8 years ago by cpad011213k
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