Reference Fasta vs Alt Reference Fasta

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Linda Do

• January 29, 2021 21:56

Hi!

Questions category: What does (......) mean?

I'm new to GATK and I was trying to follow this tutorial: https://gatk.broadinstitute.org/hc/en-us/articles/360037498992--How-to-Map-reads-to-a-reference-with-alternate-contigs-like-GRCH38

It indicates to use the alternate reference (filename with the alt label) rather than the regular reference (filename name does not have an alt label). In the resource bundle, the there are 2 references that I see: Homo_sapiens_assembly38.fasta which is 3 GB and Homo_sapiens_assembly38.fasta.64.alt which is 476.1 KB.

The second one is what I assume is the alt reference used in the tutorial but I noticed that it is significantly smaller than the first reference. Should I be combining these references before alignment in the tutorial? What exactly are the differences between the 2 references in the resource bundle? Does the first one have alternate contigs and decoys? What does the alt reference in the tutorial refer to?

Thank you in advance.

 

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  Bhanu Gandham

  • January 29, 2021 22:26

  Linda Do

  The .alt fine is not the alt reference, it is a BWA index file.

  For info on what we provide as resources take a look at this doc: https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle. 

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  Linda Do

  • February 01, 2021 19:35

  Thank you. I was under the wrong impression that the filename formats were the same. You helped me understand.

  Thank you

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