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How to check normal BAM_files before create a Panel Of Normals (PoN)

Hi, everyone hope everything is fine. I would like to ask if there's anyone who can help me about the procedure of checking BAM_files from normal samples before creating a Panel Of Normal for the variant calling step.gatk command I've tried to check with those gatk tools then calculate the Standard_deviation(std) and Mean of Log2_copy_ratio. I've also give as threshold for Std (<=0.15) but it give me high values than the threshold for all samples.

gatk variant_calling pon
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written by AIMAR • AIMAR

add your command as text not as image

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written by 1769mkc 1769mkc

Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below), or use a GitHub Gist if the content volume exceeds allowed length here.

code_formatting

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written by Pierre Lindenbaum Pierre Lindenbaum

Understood sir.

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written by AIMAR • AIMAR

I've 12 normal samples. Thanks for the share

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written by AIMAR • AIMAR

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