Malformed VCF file at approximately line number 101449: The VCF specification does not allow for whitespace in the INFO file

Question

[bruseq]

Hello

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.

Thanks..

[bruseq]

Thank you so much both of you for your valuable help to sort this error. I remove all the present whitespace in my file in info column. but when I execute this below command , it generate an empty output files of cpg.vcf and snp.vcf.

Command used:

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

Is there any suggestion how I sort this error.

Thanks in advance.

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

Answer 1

[dariober]

Philipp Bayer's solution is good but since the error says "approximately at line number ...", the offending line maybe somewhere else. Also there might be other buggy lines. This awk script will print lines where the 8th field contains a space and it will print the line number as well:

awk -v FS='\t' '$8 ~ " " {print $0, NR}' snp.raw.vcf

Answer 2

[Philipp Bayer]

Run this command:

head -101449 /home/genomics2/tool/dbSNP/snp.raw.vcf | tail -1

To see the line it complains about, then see what the error is (something borked in the INFO field?) then fix it.