Variant calling tool for Bacterial NGS data
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7 months ago
Boberoni ▴ 10

Hi everyone,

I am working on a cell line authentication project to identify different aspects (verify organism, the genome does not differ too much from reference, etc.) of a cell line that is used.

As a test I am using samples of Staphylococcus aureus, Illumina reads 150bp.

  • For QC I used Trimmomatic for adapter removal and quality trimming.
  • BWA MEM for mapping.
  • Samtools sort on chromosomal coordinates for sorted bam file.
  • GATK ( for Marking duplicates, which is using Picard.
  • No base recalibration since my quality is fairly high (>34) and there are no known SNP sites for this organism (or at least what I could find (e.g. dbSNP))

Currently, I am looking into GATK ( to use for variant calling as well. To my understanding, GATK Haplotypecaller is for germline variant calling (so single chromosomes) so this would be best applicable for S. aureus since it also has one chromosome? Or is this assumption totally incorrect and should I use Mutect2 (somatic cells) instead?

Or is GATK not the best tool for this kind of microbial data?

I am fairly new to variant calling so any answers or advice are helpful! :)

Best regards,


SNP Variant calling Bacterial GATK • 309 views
Entering edit mode

Since you are working with bacteria why not simply use bcftools (LINK)?

Entering edit mode

Thanks for your response GenoMax.

Could you explain to me why bcftools would be more suitable? Perhaps with some literature proof?


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