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SelectVariants error

niuguohaoniuguohao Member
edited December 2017 in Ask the GATK team

I`m calling SNP by haplotype caller,and i got vcf document for each sample. After that , i use selectvariant to select variants of SNP . But i got this error:

##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.8-0-ge9d806836): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Line 33910: there aren't enough columns for line  (we expected 9 tokens, and saw 1 ), for input source: /home/gaotiangang/niuguohao/1204recall/50/BQSRc/seq164.raw.c.vcf

The 33910 line is:

DF384195.1  374 .   G   A   243.77  .   AC=1;AF=0.500;AN=2;BaseQRankSum=2.100;ClippingRankSum=0.000;DP=95;ExcessHet=3.0103;FS=6.236;MLEAC=1;MLEAF=0.500;MQ=40.68;MQRankSum=-2.037;QD=7.62;ReadPosRankSum=1.274;SOR=2.712    GT:AD:DP:GQ:PL  0/1:18,14:32:99:272,0,411

I don't think there is any thing wrong with this line for the lines before it look the same.
Only part of the samples' vcf documents have this error . But i didn't find the difference between them.

Anyone coule help me ?
Many thanks!

Post edited by Geraldine_VdAuwera on

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