GATK vcf file

Question

[vicky]

Hi All

Can some body help me in converting the GATK vcf file to be used with vcfutils.pl to make fastq file. I am getting the following error.

Use of uninitialized value $q in addition (+) at /home/vicky/bin/vcfutils.pl line 518, <> line 1402.
Use of uninitialized value $q in numeric lt (<) at /home/vicky/bin/vcfutils.pl line 508, <> line 1403.

If any tool is available to do this kind of conversion. Both are the ##fileformat=VCFv4.1 still the GATK vcf file is not compatible with vcfutils.pl.

Thanks

[Zev.Kronenberg]

Please provide the whole command line you used. Are you sure you are going to FASTQ? It would make more sense if you are trying to generate FASTA.

[vicky]

Thanks for your reply . I used this command in samtools

vcfutils.pl vcf2fq GATK_vcf_file >out.fq

Actually I want to generate the consensus fasta file only. How I can do that?

Answer 1

[Ashutosh Pandey]

I read somewhere that vcf2fq option only works with samtools all-site BCF/VCF. This is the usage:

vcfutils.pl vcf2fq [options] <all-site.vcf>

So if your VCF file only contains variant sites, then vcf2fq will throw some error. You may have to use EMIT_ALL_SITES option when calling variants using GATK Unified Genotyper.

[vicky]

Thanks Ashutosh for the reply. I tried ("EMIT_ALL_SITES") that also but again I am getting the same error.

I just read Gatk Vcf File To Consensus Sequence Use Vcfutils.Pl, the same thing has been asked earlier. There some one mentioned that I need to include the FQ value which is "I find the FQ==QUAL-3". Still I don't find this thing in manual of samtools or GATK.

Answer 2

[Paweł Sztromwasser]

If you're trying to make a consensus fasta, you might want to look at GATK's FastaAlternateReferenceMaker. Haven't used it myself, but it looks relevant. And there is a chance that it will work fine with GATK's own vcf;)

[vicky]

The problem with the FastaAlternateMaker is that it is not for consenus making. It just put the SNPs in the fasta file which it makes with the help of Reference fasta file.