Hg19 and hg38 alt contigs

[Asma Rabe]

Hi,

Are there any recommendations for calling Germ line variants using hg38. We have data mapped using hg19 and l think we can use it for calling germ line variants though I know there are many more alt contigs in hg38. Any recommendations?

Thank you.
Rabe

[Matthew Speir]

Hello, Rabe. 

Thank you for your question about alt contigs in human genome assembly hg38.

If you are concerned about alignments to alt sequences in the hg38, then you may want to look into the "Analysis Set": http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/. You can find more information in our FAQ: https://genome.ucsc.edu/FAQ/FAQdownloads.html#downloadAnalysis. It removes the "alt" and "fix" sequences from the sequence files, among other changes. 

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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