How to calculate VAF from BAM or SAM(+pileups) files using pysam?

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3.9 years ago

askif4 ▴ 20

I assume pysam is a tool for BAM, SAM file.

But since the official document is a bit hard to understand. I am having difficulties calculating VAF values with pysam.

If you could suggest to me some scripts or documents, it would be grateful.

Thank you.

(It would be better if the method is restricted to using mainly pysam; not pysamstats.)

SNP sequencing bam VAF pysam • 1.5k views

ADD COMMENT • link 3.9 years ago by askif4 ▴ 20

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Don't you need to do variant calling before you can calculate VAF?

ADD REPLY • link 3.9 years ago by Ram 44k

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I already have the location of the mutations, which means I have VCF files from BAM files I know that there are other methods to calculate VAF(using VCF files), even if it is not efficient, I want to use pysam. Thanks~

ADD REPLY • link 3.9 years ago by askif4 ▴ 20

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I see. Thanks for the update. I don't know how to calculate VAF using pysam - others on the forum might be able to help you.

ADD REPLY • link 3.9 years ago by Ram 44k

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