HC_ERC output question:"sample1"

IrantzuIrantzu Member
edited January 2015 in Ask the GATK team

Hi there,

This is maybe a silly question but I want to know if it is normal or not. I have just run HC in GVCF mode for each of my bam files. When I see the output...:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1

Is it normal to have "sample1" instead of "bam file name" or something like that? I have realized because when I was running GenotypeGVCFs, I was only getting one column named also "sample1", instead of one column per input vcf (what I think that is the normal output, isn't it? So, what I've done is to change "sample1" of each vcf file with the corresponding sample name to run GenotypeGVCF.

I hope I've explained myself more or less.

Thanks in advance

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