Hi everyone,

I have 2 data sets (in FASTQ) of 2 samples with contrast phenotype. I could possibly perform these workflows:

1. Map 2 data sets to a reference transcriptome (not genome), processing individual BAM files, run GATK HaplotypeCaller, got 2 vcf files output, merge 2 vcf files into final one with vcf-merge.

2. Map 2 data sets to a reference transcriptome (not genome), processing individual BAM files, merge 2 BAM files into one with samtools, run GATK HaplotypeCaller, get 1 final vcf file output.

I would like to ask: Is there any different in final vcf files of 2 workflows? If yes, how they are different?

Thank you very much in advance.

Phuong.