Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

FilterVariantTranches Error: 'no variants with INFO score key "CNN_2D"'

Answered
1

7 comments

  • Avatar
    Genevieve Brandt (she/her)

    Hi Cher Wei Yuan,

    Hmmm, interesting. I'm not exactly sure what's going on here, but I'll help to figure it out! All the lines you shared from your VCF file are from non-variant reference blocks. Could you share any lines that have variance with the CNN_2D key?

    Best,

    Genevieve

    0
    Comment actions Permalink
  • Avatar
    Cher Wei Yuan

    Hi Genevieve
    Thank you so much. Here are two lines with variance:


    chr7 96317809 . TA T,<NON_REF> 798.04 . BaseQRankSum=0.929;CNN_2D=-10.974;DP=189;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=680400,189;ReadPosRankSum=2.347 GT:AD:DP:GQ:PL:SB 0/1:97,59,0:156:99:853,0,3018,1121,3297,4596:41,56,24,24
    chr7 96317810 . AT *,A,TT,ATT,<NON_REF> 0 . BaseQRankSum=-0.177;CNN_2D=-13.423;DP=191;ExcessHet=3.0103;MLEAC=1,0,0,0,0;MLEAF=0.500,0.00,0.00,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=687600,191;ReadPosRankSum=0.910 GT:AD:DP:GQ:PL:SB 0/1:70,60,3,9,2,0:144:99:2341,0,2585,2335,1988,4355,1412,2283,3152,3772,2563,1936,4190,3226,4630,2525,2380,4333,3641,4456,4723:29,41,34,40

     

    Please let me know if more information is required.

    Best Regards

    Cher Wei Yuan

    0
    Comment actions Permalink
  • Avatar
    Amatta Mirandari

    Hi I am receiving the same error using GATK-4.2.2, but with CNN_1D. e.g.

    A USER ERROR has occurred: Bad input: VCF contains no variants or no variants with INFO score key "CNN_1D"

    This is despite having checked the VCF file and finding the CNN_1D tag both in the header and INFO fields of most variants. 

    Thank you 

    0
    Comment actions Permalink
  • Avatar
    Genevieve Brandt (she/her)

    Thanks for providing the information Amatta Mirandari!

    Is your file also a GVCF file? I'm trying to piece together why this is occurring. 

    0
    Comment actions Permalink
  • Avatar
    Genevieve Brandt (she/her)

    Hi Cher Wei Yuan,

    I discussed this issue with the developer team who works on CNNScoreVariants. The input to CNNScoreVariants is supposed to be a VCF file. We have not tested CNNScoreVariants on GVCFs, so this may be why you are getting the error message. You can genotype your GVCF with GenotypeGVCFs or you can go back to the HaplotypeCaller step and remove the -ERC BP_RESOLUTION argument.

    Please let me know if for some reason you are still having this error with a VCF file or if you have further questions.

    Best,

    Genevieve

    0
    Comment actions Permalink
  • Avatar
    Cher Wei Yuan

    Hello Genevieve Brandt (she/her)

    I did not realized my HaplotypeCaller parameters output a gvcf. I removed "-ERC BP_RESOLUTION \
    -GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 50 -GQB 60 -GQB 70 -GQB 80 -GQB 90" and re-run the HaplotypeCaller and the remaining workflow. Everything works now! Thank you for your help.

    Best Regards

    Wei Yuan

    0
    Comment actions Permalink
  • Avatar
    Genevieve Brandt (she/her)

    Glad to hear we could solve the issue! Thanks for the update.

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk