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 availble to do this kind of conversion. Both are the ##fileformat=VCFv4.1 still the GATK vcf file is not compatible with vcfutils.pl.
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;)