From Fastq to vcf
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3.7 years ago
yakko • 0

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

alignment sequencing Fastq • 562 views
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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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3.7 years ago
MatthewP ★ 1.4k

Hello, this post from GATK suggest hard-filtering.

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