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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

GetPileupSummaries raised an error: htsjdk.tribble.TribbleException


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    Genevieve Brandt (she/her)

    Hi Hiro Ama,

    Thanks for writing into the forum so that we can get GATK working for you!

    I looked closer at the error message and it looks like this issue is with your GNOMAD file (gnomad.exomes.r2.1.1.sites_withchr.vcf.gz). It looks like there was an issue when you replaced the chromosome names because part of the INFO field of the line mentioned here was replaced with another line and not properly ended. That is why there is whitespace in the INFO field, which will not work with GATK.

    Here is the snippet of the field where the whitespace occurs:

    non_cancer_AC_female=9;non_cancer_AN_female=88070;non_cancer_AF_female=0.000102191;non_cancer_nhomalt_female=0;non_cachr16 2549972 rs370235069 T A 50080.7 PASS AC=26;AN=248606;AF=0.000104583;rf_tp_probability=0.918423;FS=0;InbreedingCoeff=0.0028;MQ=59.4;MQRankSum=0.22;

    If you get this fixed properly you should have no issues with this file.



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