BWA and samtools and bcftools for exome sequencing?

Question

[Dayna]

Hi everyone

I used bwa, samtools, and bcftools for exome sequencing analysis to generate vcf. Want to know whether this is still correct and okay, and how this is different from GATK pipeline?

Thanks

[Kevin Blighe]

Depends on how you've used these programs. Can you post some commands, particularly at the variant calling step?

From my experience, SAMtools/BCFtools is better for calling Sanger-confirmed SNVs than GATK, but not indels.

Answer 1

[Medhat]

To have better results I think you need to do the recalibration step.
as shown here http://www.htslib.org/workflow/

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More:
Systematic comparison of variant calling pipelines using gold standard personal exome variants

Detailed comparison of two popular variant calling packages for exome and targeted exon studies

Validation and assessment of variant calling pipelines for next-generation sequencing

Difference Between Samtools And Gatk Algorithms

Difference Between GATK, Freebayes and SAMtools mpileup

[WouterDeCoster]

Gasp, a non-proportional Venn diagram ;o

[Medhat]

but, the numbers are clear !

[WouterDeCoster]

Yes, but being non-proportional you could as well put it in a table and be as clear as this venn diagram.