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Variant Discovery in High-Throughput Sequencing Data

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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

VariantAnnotator Follow

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    Hello, GATK team.

    I'd like to request assistance with resolving an error that I faced while using the GATK Annotator tool.

    I encountered an error "ava.lang.IllegalArgumentException: Null alleles are not supported" and proceeded with annotator using the command listed below.

    java -Dfile.encoding=ISO-8859-1 -Xmx200g -jar -DGATK_STACKTRACE_ON_USER_EXCEPTION=true gatk-package- VariantAnnotator -R ${genome.fa} -V ${vcf} --dbsnp ${dbSNP156| -O ${result_vcf}

    Upon my inspection, the analysis halted at the genotype "1/." position.
    The input VCF file was generated by Strelka2 and originally had genotypes as 1/2 at multiallelic positions.
    After multiallele split, each position changed to "1/." and "./1".
    I found it puzzling that while some variants in the same situation were annotated normally, certain variants encountered errors like below.

    ## Annotator Fail variant case

    [ Before the split multi allele.]

    chr1    4531725 .       ATAC    AC,AT   205     PASS    CIGAR=1M2D1M,2M2D;RU=AT,AC;REFREP=1,14;IDREP=0,13;MQ=60 GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL  1/2:49:4:22:2,11,9:0,6,4:2,5,5:PASS:284,89,116,122,0,93

    [ After multi allele process ]

    chr1    4531725 .       ATAC    AC      205     PASS    CIGAR=1M2D1M;RU=AT;REFREP=1;IDREP=0;MQ=60       GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL  1/.:49:4:22:2,11:0,6,4:2,5,5:PASS:284,89,116
    chr1    4531725 .       ATAC    AT      205     PASS    CIGAR=2M2D;RU=AC;REFREP=14;IDREP=13;MQ=60       GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL  ./1:49:4:22:2,9:0,6,4:2,5,5:PASS:284,122,93

    ## Annotator pass variant case

    chr1    1002415 .       C       CATTT,CATTTT    692     PASS    CIGAR=1M4I,1M5I;RU=ATTT,ATTTT;REFREP=0,0;IDREP=1,1;MQ=60        GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL  1/2:94:19:46:0,12,10:0,11,3:0,1,7:PASS:771,226,131,261,0,170

    ====> Multi allele process ===> 

    chr1    1002415 rs1553168963    C       CATTT   692     PASS    CIGAR=1M4I;DB;IDREP=1;MQ=60;REFREP=0;RU=ATTT    GT:AD:ADF:ADR:DPI:GQ:GQX:PL     1/.:0,12:0,11,3:0,1,7:46:94:19:771,226,131
    chr1    1002415 rs1553168963    C       CATTTT  692     PASS    CIGAR=1M5I;DB;IDREP=1;MQ=60;REFREP=0;RU=ATTTT   GT:AD:ADF:ADR:DPI:GQ:GQX:PL     ./1:0,10:0,11,3:0,1,7:46:94:19:771,261,170


    1. I wonder what criteria the annotator has to decide that there is no null allele, so it stops.
    2. Is there any way to solve the above error?
    3. In the case of vcf created by Haplotypecaller, the above error was not identified. Is it an error that occurred because the contents of FORMAT were different depending on the caller?

    I look forward to your reply. 

    Thank you.

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