Software to detect snps and indels on pacbio data

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5.5 years ago

kamel ▴ 70

Dear colleagues,

I want to detect SNPs and Indels on pacbio data (I did the subreads mapping on the reference sequence by minimap). Do you have an idea about the tools that identify variations on pacbio data ???

snp indels pacbio • 1.8k views

ADD COMMENT • link 5.5 years ago by kamel ▴ 70

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Did you try searching the internet for it? Or google scholar? Like:

https://scholar.google.com/scholar?as_ylo=2017&q=snp+pacbio&hl=en&as_sdt=0,5

Previous similar question:

long reads Pacbio SNP calling

ADD REPLY • link 5.5 years ago by h.mon 35k

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No information about my question in this post

ADD REPLY • link 5.5 years ago by kamel ▴ 70

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The link on the bottom contains a link to the GitHub of PacificBiosciences and its toolkit GenomicConsensus, which apparently contains a variant calling module. Please do put in a bit of effort reading the linked posts before replying to a user in such an unmotivated fashion. This might make you appear lazy and does not motivate others to help you any further.

ADD REPLY • link 5.5 years ago by ATpoint 81k

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