Question: samtools variant calling
0
gravatar for 897598644
5.8 years ago by
89759864490
China
89759864490 wrote:

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!

ADD COMMENTlink modified 5.8 years ago by iraun3.8k • written 5.8 years ago by 89759864490
2
gravatar for iraun
5.8 years ago by
iraun3.8k
Norway
iraun3.8k wrote:

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: https://www.broadinstitute.org/gatk/guide/article?id=1259

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

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by iraun3.8k
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