Question

samtools variant calling

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Entering edit mode

9.6 years ago

897598644 ▴ 100

Excuse me :

After calling variants with samtools and bcftools, I got vcf file. Could I recalibrate the variants using VQSR procedure? Is it practicable?

Many thanks in advance!

alignment next-gen-sequencing sequence • 1.9k views

ADD COMMENT • link updated 2.7 years ago by Ram 44k • written 9.6 years ago by 897598644 ▴ 100

Ram · Answer 1 · 2015-05-28

From GATK documentation:

Which training sets / arguments should I use for running VQSR?

These recommendations are valid for use with calls generated by both the UnifiedGenotyper and HaplotypeCaller. These recommendations will probably not work properly on calls generated by other (non-GATK) callers.

Read here for more info.

So... you can try and check if it works, but taking into account that is not the recommended workflow.