BWA and samtools and bcftools for exome sequencing?
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4.0 years ago
Dayna ▴ 20

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

exome sequencing • 1.5k views
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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.

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Gasp, a non-proportional Venn diagram ;o

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but, the numbers are clear !

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

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