GATK Variant Recalibrator ERROR

Could someone please provide me with a help to run Variant Recalibrator for GATK4.0.11.0?
when running the tool using GATK with the following command line:

time ~/gatk- VariantRecalibrator
-R ~/reference/hg19.fa -V ~/MT-1/outname.HC.vcf.gz
--resource hapmap,known=false,training=true,truth=true,prior=15.0:~/reference/hg19/hapmap_3.3.hg19.sites.vcf
--resource omni,known=false,training=true,truth=false,prior=12.0:~/reference/hg19/1000G_omni2.5.hg19.sites.vcf
--resource 1000G,known=false,training=true,truth=false,prior=10.0:~/reference/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf
--resource dbsnp,known=true,training=false,truth=false,prior=6.0:~/reference/hg19/dbsnp_138.hg19.vcf
--use-annotation DP --use-annotation QD --use-annotation FS --use-annotation SOR --use-annotation ReadPosRankSum --use-annotation MQRankSum
--mode SNP
--truth-sensitivity-tranche 100.0 --truth-sensitivity-tranche 99.9 --truth-sensitivity-tranche 99.0 --truth-sensitivity-tranche 95.0 --truth-sensitivity-tranche 90.0
--rscript-file ~/MT-1/outname.HC.snps.plots.R
--tranches-file ~/MT-1/outname.HC.snps.tranches
--output ~/MT-1/outname.HC.snps.recal

I met this questiion: A USER ERROR has occurred: Couldn't read file file:///home/chenjie1/~/reference/hg19/hapmap_3.3.hg19.sites.vcf. Error was: It doesn't exist

The command syntax follows the same pattern as version
Has the syntax been changed for GATK version
Best regards.

Best Answers


  • bhanuGandhambhanuGandham Member, Administrator, Broadie, Moderator admin

    Hi @JieChen

    The error looks like it has to do with the hapmap vcf file and not the syntax.
    Would you please post the result of ls -l ~/reference/hg19
    Thank you.


  • JieChengJieCheng Member

    Hi @Bhanu

    Here are the result of ls -l ~/reference/hg19.

    total 21673492
    208737488 11月 2 13:36 1000G_omni2.5.hg19.sites.vcf
    1529200 11月 2 13:27 1000G_omni2.5.hg19.sites.vcf.idx
    242018150 11月 2 13:36 1000G_phase1.indels.hg19.sites.vcf
    1238920 11月 2 13:29 1000G_phase1.indels.hg19.sites.vcf.idx
    7398865818 11月 5 09:49 1000G_phase1.snps.high_confidence.hg19.sites.vcf
    10796220779 11月 3 13:14 dbsnp_138.hg19.vcf
    12381528 11月 2 13:38 dbsnp_138.hg19.vcf.idx
    238391040 11月 6 11:49 hapmap_3.3.hg19.sites.vcf
    2618906 11月 2 13:40 hapmap_3.3.hg19.sites.vcf.idx
    90196895 11月 2 13:45 Mills_and_1000G_gold_standard.indels.hg19.sites.vcf
    1484596 11月 2 13:46 Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.idx
    12689 11月 3 15:07 ucsc.hg19.dict
    3199905909 11月 3 16:35 ucsc.hg19.fasta
    3534 11月 2 13:24 ucsc.hg19.fasta.fai
    1430 11月 2 17:12 wget-log
    3812 11月 2 17:32 wget-log.1

    Thank you.

    Best regards.

  • JieChengJieCheng Member


    I found that maybe I found the cause of this problem. This is because I'm not getting shell expansion of the "~" now because its embedded. I tried expanding that manually on the command line. It worked.

    But I met a new problem. It is

    A USER ERROR has occurred: Input /home/chengjie1/reference/hg19/1000G_phase1.snps.high_confidence.hg19.sites.vcf must support random access to enable queries by interval. If it's a file, please index it using the bundled tool IndexFeatureFile

    I tried to find a way to solve this problem online, but it seems that there is no good result. Could you please give me some guidance on this issue? Many thanks.

    Best regards.

  • JieChengJieCheng Member

    Hi @Bhanu
    It works.
    Thank you for your help.

    Best regards.


  • JieChengJieCheng Member

    Hi @Bhanu
    Sorry to ask you again. Do you know how to call GATK on the GPU? My lab wants to try to use GATK on the GPU to see if there is any way to get GATK to complete the genetic analysis process faster. Could you please provide some help in this direction? Thank you again.

    Best regards.

  • JieChengJieCheng Member

    Hi @bhanuGandham

    Thank you for your help.
    Best regards.


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