multiple fastq files for a sample produced same number of columns in vcf, how can we produce one?

Hello,

I have multiple sequence files for a sample:
sample1: 1.fastq; 2.fastq, 3.fastq
sample2: 4.fastq; 5.fastq

I did the alignment with CLC genomics and called SNPs with GATK. The input was two alignment files: sample1.bam and sample2.bam. I am getting 5 columns of SNP data as sequence names mentioned above in vcf output.
How can I say GATK that each bam is a single sample not the sequence file names in the alignment?

Thank you
Sandesh