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Error when running VariantRecalibrator

Hi,
I'm running the VariantRecalibrator with input HC gVCF file that was created by GenotypeGVCFs on a list of 66 samples. I'm getting an error message: "MESSAGE: Line 474547: there aren't enough columns for line".

All input vcf lines contain the same #columns. I tried the same command several times and got same error message with different line number.
also, the same command that I used with another input file (with less samples, 57), is running fine.
Please advise - are there parameters I should change to handle a larger input file?

Thanks,
Lily

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @Lily‌

    Hi,

    Are you using the latest version of GATK?

    Can you post all the commands you used? Please post your commands for Haplotype Caller and all the steps after it.

    Also, can you post the record at line 474547?

    Thanks,
    Sheila

  • LilyLily Member

    Hi Sheila,

    I'm using GATK 3.2.2
    I found a problem in the HC gVCF file. It contains a line full of @s in the middle. I don't know what caused it. it I'm currently re-running the GenotypeGVCFs to re-create this file with the same sample list. I hope to get a better result now...

    My GenotypeGVCFs command is:
    nohup java7.1 -Xmx32g -jar gatk-3.2.2/GenomeAnalysisTK.jar -T GenotypeGVCFs -R ucsc_hg19.fa -D dbsnp135_hg19.vcf -V HC_gVCFs.list -o HC_gVCFs.out

    Thanks,
    Lily

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