From Fastq to vcf

Hi, While calling variants the last suggested step from gatk is the Recalibration. What should I expect without this filter? Thanks.

alignment sequencing fastq

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updated 6.1 years ago by MatthewP

• written 6.1 years ago by yakko •

While I am pretty sure I can't answer that question for you, you may consider to change the title of your post. It does not really match your actual question now.

Did you also found this page already? https://gatk.broadinstitute.org/hc/en-us/articles/360035890531-Base-Quality-Score-Recalibration-BQSR-

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written 6.1 years ago by gb

1 answer

Hello, this post from GATK suggest hard-filtering.

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written 6.1 years ago by MatthewP

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