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Malformed VCF file

divya_infodivya_info LucknowMember

I am using BisSNP-0.82.2 tool to find SNP in bisulfite data. But I get the below mention error while using this command : java -Xmx4g -jar BisSNP-0.82.2.jar -R /home/genomics2/ALM_BS_genome_new.fasta -T BisulfiteGenotyper -I /home/genomics2/tools/ALM1Fd_R1_paired_trimmed_withRG.bam -D /home/genomics2/tools/dbSNP/merge_vcf_file2.vcf -vfn1 /home/genomics2/tool/dbSNP/cpg.raw.vcf -vfn2 /home/genomics2/tool/dbSNP/snp.raw.vcf -L /home/genomics2/tools/ALM1_R1_paired_vcf_lenght.bed

ERROR MESSAGE: The provided VCF file is malformed at approximately line number 101449: The VCF specification does not allow for whitespace in the INFO field.

Please guide me how to sort this error.

Best Answer


  • divya_infodivya_info LucknowMember

    @Geraldine_VdAuwera Thank you so much for your guidance, I have sort this error by remove all spaces present in my file of info column, but when I execute this below command :
    java -Xmx4g -jar BisSNP-0.82.2.jar -R /home/genomics2/tools/For_METHGO/ALM_BS_genome_new.fasta -T BisulfiteGenotyper -I /home/genomics2/tools/For_METHGO/ALM1Fd_R1_paired_trimmed_withRG.bam -D /home/genomics2/tools/For_METHGO/dbSNP/merge_new_dbSNP21.vcf -vfn1 /home/genomics2/tools/For_METHGO/dbSNP/cpg1.raw.vcf -vfn2 /home/genomics2/tools/For_METHGO/dbSNP/snp1.raw.vcf -L /home/genomics2/tools/For_METHGO/ALM1_R1_paired_vcf_lenght.bed

    The output files i.e; cpg.vcf and snp.vcf generate is empty. Any suggestion how I sort the problem.

    Thanks :smile:

  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin


    Bis-SNP is not our tool. You will have to ask the developers of the tool for help.


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