Hello All,

I tried to call GTAK 'HaplotypeCaller gvcf mode' and it ran successfully. Output gvcf file showing the following header information

########fileformat=VCFv4.2
########ALT=ID=NON_REF,Description="**Represents any possible alternative allele not already represented at this location by REF and ALT**"

I checked with some other gvcf file in online, including GATK example file, and it showing the ALT header as

########fileformat=VCFv4.2
########ALT=ID=NON_REF,Description="**Represents any possible alternative allele at this location**".

Please can somebody tell me that is there any mistake in my output gcVF file or is it normal ?

GTAK command used for Haplotype call : gatk-4.1.7.0/gatk HaplotypeCaller --java-options '-Xmx10G' -R pdsk_genome.fa -I w_00001.bam -O wgs_00001.g.vcf -ERC GVCF --minimum-mapping-quality=20 --min-base-quality-score=20 --tmp-dir=tmp