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Mapping /aligning reads to a custom genome

I had whole genome sequencing done using next generation sequencing  for a person i'm studying for a research project. Does IGV(integrative Genomics Viewer) have  a way to replace the hg19 reference genome with a custom reference genome? If yes, how can I map /align the reads of my patient's to this custom reference genome on IGV?

Thank you

next-gen alignment
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written by Adeler001 • Adeler001

You can define/use a custom genome in IGV by following these directions.

If yes, how can I map /align the reads of my patient's to this custom reference genome on IGV?

But you will need to first assemble the reads to create that custom genome yourself. Mapping does not happen in IGV. You will need to do mapping yourself.

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written by GenoMax GenoMax

How would I go about mapping the reads myself?

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written by Adeler001 • Adeler001

Re-reading your original post it sounds like you already have a custom genome you want to use. Use an aligner (noted below) to align the reads to the genome. You will need to create aligner indexes for the custom genome before doing the alignments.

If you can align to to an existing reference (like GRCh38 or hg19) then use an aligner (BWA, bbmap etc) with your data. You can use pre-made indexes in this case. e.g. they can be found on Illumina's iGenomes site.

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written by GenoMax GenoMax

Hello genomax thank you for responding. Yes, I already have the custom reference genome I want to use. What I'm trying to do is align the patient's genome to my custom reference genome.

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written by Adeler001 • Adeler001

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