Question: Merging BAM file before running GATK or merging vcf output
0
gravatar for pbigbig
2.2 years ago by
pbigbig200
United States
pbigbig200 wrote:

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.

snp gatk vcf • 1.4k views
ADD COMMENTlink modified 2.2 years ago by Lila M 800 • written 2.2 years ago by pbigbig200
0
gravatar for Lila M
2.2 years ago by
Lila M 800
UK
Lila M 800 wrote:

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.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Lila M 800
1

thank you for your opinion!

ADD REPLYlink written 2.2 years ago by pbigbig200
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