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

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22 days ago

AIMAR • 0

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 • 582 views

ADD COMMENT • link 22 days ago by AIMAR • 0

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add your command as text not as image

ADD REPLY • link 22 days ago by 1769mkc ★ 1.3k

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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

ADD REPLY • link 22 days ago by Pierre Lindenbaum 166k

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Understood sir.

ADD REPLY • link 22 days ago by AIMAR • 0

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Do you have enough samples to create a private PON? GATK recommends a minimum of 40. If not you can use public 1000 genomes PON.

https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON