Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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

crop_bioinfocrop_bioinfo knoxvilleMember
edited January 2017 in Ask the GATK team


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


Sign In or Register to comment.