Chromosome name of db SNP hg38 build for Funcotator

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Apprentice

• March 29, 2020 08:49
• Edited

Hi.

I always appreciate you.

I obtained funcotator_dataSources.v1.6.20190124s.tar.gz to use funcotator using a below command. 

 

The chromosme names were coded as chr1, chr2, chr3, chr4, ... in the file funcotator_dataSources.v1.6.20190124s/dbsnp/hg19/hg19_All_20170710.vcf.gz. 

However, I noticed that the chromosme names were coded as 1,2, 3, 4, ... in the file funcotator_dataSources.v1.6.20190124s/dbsnp/hg38/hg38_All_20170710.vcf.gz. 

Could you correct it in the hg38 dbSNP file?

 

Can you please provide
a) GATK version used : 4.1.6.0

b) Exact GATK commands used :

java -Xmx5g -jar gatk-package-4.1.6.0-local.jar FuncotatorDataSourceDownloader --somatic --validate-integrity --extract-after-download

c) The entire error log if applicable.

Nothing

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  Bhanu Gandham

  • April 01, 2020 16:33

  HI Apprentice

   

  We are looking into this. It might take until Monday to get around to fixing it. I wanted to keep you posted on the timeline. 

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  Joe Hiatt

  • April 01, 2020 23:02

  im having the same problem. appreciate the efforts to fix!

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  Apprentice

  • April 02, 2020 05:32
  • Edited

  Thank you for your reply.

  I'm look forward to getting corrected data on Monday.

   

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  Bhanu Gandham

  • April 06, 2020 18:04

  Hi,

   

  We are still working on this issue and might take us a while to resolve it. Not sure on the timeline for this just yet. This issue is with NCBI hg38 dataset and if you download it directly from NCBI too you will see the same issue. We are however trying to resolve this on our end and will have an update for you soon.

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