Filtering SNPs from haploid assembly

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4.0 years ago

drowl1 ▴ 30

Hi All!

I have a task that I am at the moment not able to figure out how to go about. I am a beginner so apologies if this seems trivial.

I have a VCF file with SNPs called by Freebayes for 24 haploid nuclei, with each nuclei representing an individual sample. Now I want to filter the SNPs so that to keep those SNPs that are supported in an individual nucleus at > = 80%. (i.e the SNP to be supported by at least 80% of the reads at that position in the nucleus/ if they have 80% of one nucleotide at that position)

I would be very grateful if anyone would suggest how I should go about this and what tool (s) to use.

genome sequencing assembly SNP • 790 views

ADD COMMENT • link 4.0 years ago by drowl1 ▴ 30

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you asked many questions on this forum but you didn't validate any. (Green mark on the left of the answers)...

ADD REPLY • link 4.0 years ago by Pierre Lindenbaum 161k

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Its been a couple of years now, was not aware of this option until now. Apologies.

ADD REPLY • link 4.0 years ago by drowl1 ▴ 30

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No problem. It is not a strict rule but a matter of good practice and appreciation. These options do exist:

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ADD REPLY • link 4.0 years ago by ATpoint 81k

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