how can I get the small_exac_common_3_b37.vcf for GATK GetPileupSummaries
Answered
I want to download small_exac_common_3_b37.vcf for GATK GetPileupSummaries by the following two way, but it totally got worse.
1. I can't open the ftp link ftp://ftp.broadinstitute.org/bundle/
2. I can't find the file in Goole-Cloud https://console.cloud.google.com/storage/browser/genomics-public-data
So, how can I get the small_exac_common_3_b37.vcf?
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I find a vcf called funcotator_gnomAD_2.1_VCF_INFO_AF_Only_hg38_gnomad.exomes.r2.1.sites.liftoverToHg38.INFO_ANNOTATIONS_FIXED.vcf.gz in Goole-Cloud https://console.cloud.google.com/storage/browser/genomics-public-data. Does such two file are the same?
But I got error info when I run GetPileupSummaries with funcotator_gnomAD_2.1_VCF_INFO_AF_Only_hg38_gnomad.exomes.r2.1.sites.liftoverToHg38.INFO_ANNOTATIONS_FIXED.vcf.gz.
[July 13, 2021 3:08:39 PM CST] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed tim
Runtime.totalMemory()=3066036224
***********************************************************************A USER ERROR has occurred: Contig chr1_KI270706v1_random not present in reads sequence dictionary
***********************************************************************
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Hi zhan li,
I am going to move your post into our Community Discussions -> General Discussion topic, as the somatic topic is for reporting bugs and issues with GATK.
You can read more about our forum guidelines and the topics here: Forum Guidelines.
Best,
Pamela
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Hi zhan li,
Have you seen this article regarding how to access our data resources? Please take a look and hopefully it helps solve your issue. If not, I can help from there!
Best,
Genevieve
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