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[BaseRecalibrator] NCBI dbSNP incompatibility w/ Ensembl whole genome

mattqdeanmattqdean CAMember
edited February 2016 in Ask the GATK team

First, thank you for your time and help.

I downloaded dbSNP build 141 from NCBI and GRCh38.p5 from Gencode. I am using both for GATK BaseRecalibrator but I received an error caused by, I believe, 'chr' annotation.

ERROR   /00-All.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT]

ERROR   reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, GL000008.2, GL000009.2, GL000194.1, GL000195.1, GL000205.2, GL000208.1, GL000213.1, GL000214.1, GL000216.2, GL000218.1, GL000219.1, GL000220.1, GL000221.1, GL000224.1, GL000225.1, GL000226.1, KN538364.1, KQ031383.1, KN538369.1, JH159136.1, JH159137.1, KQ031387.1, KN538360.1, KN196484.1, KN196476.1, KN196479.1, KN196473.1, KN196487.1, KN196475.1, KQ090016.1, KN538361.1, KN196474.1, KQ090022.1, KN196478.1, KN196480.1, KQ090028.1, KN196483.1, KN196481.1, KN538363.1, KN538362.1, KQ031385.1, KQ031386.1, KQ031388.1, KN538365.1, KN538366.1, KN538367.1, KN538370.1, KN538373.1, KN538371.1, KQ031384.1, KN538372.1, KQ090021.1, KN196482.1, KQ458386.1, KN196472.1, GL383545.1, GL383546.1, KI270824.1, KI270825.1, KQ090020.1, GL383547.1, KN538368.1, KI270826.1, KI270827.1, KI270829.1, KI270830.1, KI270831.1, KI270832.1, KI270902.1, KI270903.1, KI270927.1, GL877875.1, GL383549.1, GL383550.2, KQ090023.1, GL877876.1, GL383552.1, KI270904.1, GL383553.2, KI270835.1, GL383551.1, KI270837.1, KI270833.1, KI270834.1, KI270836.1, KI270838.1, KI270839.1, KI270840.1, KI270841.1, KI270842.1, KI270843.1, KQ090024.1, KQ090025.1, KI270844.1, KI270845.1, KI270846.1, KI270847.1, KI270852.1, KI270848.1, GL383554.1, KI270906.1, GL383555.2, KI270851.1, KI270849.1, KI270905.1, KI270850.1, KQ031389.1, KI270853.1, GL383556.1, GL383557.1, KI270855.1, KQ031390.1, KI270856.1, KQ090027.1, KQ090026.1, KI270854.1, KI270909.1, GL383563.3, KI270861.1, GL383564.2, GL000258.2, KI270860.1, KI270907.1, KI270862.1, ... ... 
(contracted to meet character limit)

Specifically the genome sequence has 'chr' and (also unplaced contigs) but the SNP vcf file does not. I appended 'chr' using:

sed -e '/^[^#]/s/^/chr/' -e 's/^chrMT/chrM/'

Will it matter if the SNP vcf file does not included all the unplaced contigs that my reference genome has?

Also I saw that Ensembl also has publicly available variant vcf files - one has germline variants and another has somatic variants.

For the purpose of using MuTect2 for my tumor samples, are the somatic variant vcf the same thing as Sanger's COSMIC file?
If not, is it advisable to merge the two variant files into 1 SNP file?

EDIT: I also see that NCBI has a separate SNP file for unplaced contigs (should I merge the two?) and that UCSC has its own SNP (following Ensembl format) for common, clinically-associated, and multimapped variants. With so many options which would be preferable for GATK workflow using Ensembl's GRCh38 and GRCh37?

Issue · Github
by Sheila

Issue Number
Last Updated
Closed By


  • SheilaSheila Broad InstituteMember, Broadie admin



    Sorry for the late response. Someone will get back to you shortly.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there, you're trying to use incompatible resources. It's not enough to change the contig naming -- there are differences between genome reference builds. This is documented in our FAQs.

    For the rest, can you clarify what workflow you're trying to follow / what you're trying to achieve? It will help us advise you appropriately. As you observed there are many options, and we need to know more about your experiment in order to guide you.

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