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GATK vcf file compatibility in samtools vcfutils.pl

Hi

I am trying to used GATK vcf ( haplotype calller) file to use 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 in GATK to do this kind of conversion. If both are the ##fileformat=VCFv4.1 why the GATK vcf file is not compatible with vcfutils.pl.?

Answers

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