Does default hg38 build version contain alt contigs? A note on built-in reference genomes


Does the default hg38 build version available on contain alt contigs? I am getting zero mapping quality at a particular target whereas mapping against hg19 results in passable quality. Mapper is bwa mem. Is there an option to use only toplevel sequence? And if there is no mention of the type of build used as default (I didn’t find any), it’s probably a good idea to include it.

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Hello @prishly!

Both hg19 and hg38 are sourced from UCSC. The base build for both contain the full chromosome set. See:

There used to be a message on tool forms that contained an explanation about genome builds but this has been omitted on updated tools. I’ll look into getting that added in. Agree that this information could be easier to find.

FAQ with info:

Screenshot of Map with Bowtie for Illumina help form. This is the info that I think could be added again across mapping tools.

How to map against the “Canonical” or “Canonical Female” version of the hg38 build:


Ticket opened to address the tool form documentation: