Merging BAM file before running GATK or merging vcf output

Question

[pbigbig]

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.

Answer 1

[Lila M]

You can find your answer here!

For me, the best option if you have different samples is to run HaplotypeCaller independently for each bam file and then merge the vcfs files.

[pbigbig]

thank you for your opinion!