Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

The provided VCF file is malformed at...

naarkhoonaarkhoo Posts: 37Member

My question could seems like here but, the answer didn't help me.

I am using VariantFiltration over a VCF file which is generated directly after UnifiedGenotype under GenomeAnalysisTK-2.3-9-ge5ebf34.

The error I am facing is

##### ERROR MESSAGE: The provided VCF file is malformed at approximately line number 126: there aren't enough columns for line 70 (we expected 9 tokens, and saw 1 )

Line number 126 is as following,

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  m1016ROUa.40287 m1023ROGa.40244 m1042ujba.40261 m1069FXFa.49470

And actually indeed it is the header of VCF file ! Should I re-run my samples ?!!

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,210Administrator, GSA Member admin

    Hi there,

    Did you do any manipulations on the file after it was made by UG, before you got the error? UG shouldn't be generating bad vcf files.

    if you can't find the source of the error, I suggest you run your samples again with the new version (2.4).

    Geraldine Van der Auwera, PhD

  • tommycarstensentommycarstensen Posts: 49Member
    edited May 2013

    I have the same problem, except when using CombineVariants 2.4 trying to merge 4 VCFs generated with UnifiedGenotyper 2.4:

    ERROR MESSAGE: Line 4623: there aren't enough columns for line

    I haven't experienced this problem with other VCF files; i.e. other VCF files generated in the exact same way for the same samples but for different chromosome fragments. I also tried to regenerated the 4 VCF files in question.

    This is what line 4623 in those 4 VCFs look like:

    12 50240233 . A . 0.08 LowQual AN=122;DP=174;MQ=51.69;MQ0=0 GT:DP 0/0:1 0/0:4 0/0:3 0/0:1 0/0:1 0/0:2 0/0:1 0/0:5 0/0:2 0/0:1 0/0:3 0/0:2 ./. 0/0:1 0/0:1 0/0:3 0/0:1 0/0:3 0/0:1 0/0:2 0/0:1 0/0:2 0/0:1 0/0:1 0/0:3 0/0:2 0/0:2 0/0:2 0/0:4 0/0:1 0/0:6 0/0:6 0/0:3 ./. 0/0:6 0/0:3 0/0:3 0/0:3 0/0:3 ./. 0/0:3 0/0:4 0/0:2 0/0:2 0/0:4 0/0:2 ./. ./. 0/0:5 0/0:2 0/0:3 0/0:3 0/0:4 0/0:1 0/0:4 0/0:2 ./. 0/0:2 0/0:3 0/0:2 0/0:3 0/0:5 0/0:8 0/0:6 0/0:2 0/0:4 0/0:4

    12 50233207 . G . 33.96 . AN=198;DP=544;MQ=58.53;MQ0=0 GT:DP 0/0:3 0/0:8 0/0:10 0/0:9 0/0:4 0/0:6 0/0:4 0/0:3 0/0:4 0/0:8 0/0:6 0/0:5 0/0:7 0/0:3 0/0:8 0/0:2 0/0:3 0/0:2 0/0:3 0/0:4 0/0:8 0/0:2 0/0:5 0/0:3 0/0:3 0/0:6 0/0:9 0/0:6 0/0:2 0/0:4 0/0:10 0/0:6 0/0:1 0/0:7 0/0:9 0/0:6 0/0:8 0/0:5 0/0:3 ./. 0/0:4 0/0:6 0/0:5 0/0:2 0/0:8 0/0:4 0/0:6 0/0:5 0/0:9 0/0:5 0/0:6 0/0:9 0/0:3 0/0:5 0/0:4 0/0:6 0/0:10 0/0:6 0/0:7 0/0:2 0/0:8 0/0:6 0/0:9 0/0:6 0/0:2 0/0:4 0/0:4 0/0:7 0/0:6 0/0:4 0/0:5 0/0:5 0/0:4 0/0:6 0/0:3 0/0:4 0/0:5 0/0:6 0/0:6 0/0:6 0/0:9 0/0:4 0/0:4 0/0:8 0/0:8 0/0:5 0/0:8 0/0:3 0/0:2 0/0:6 0/0:8 0/0:4 0/0:5 0/0:10 0/0:12 0/0:3 0/0:6 0/0:6 0/0:3 0/0:7

    12 50233595 . T . 27.78 . AN=200;DP=563;MQ=59.33;MQ0=0 GT:DP 0/0:4 0/0:6 0/0:5 0/0:11 0/0:4 0/0:1 0/0:1 0/0:6 0/0:7 0/0:8 0/0:9 0/0:5 0/0:8 0/0:4 0/0:7 0/0:9 0/0:4 0/0:4 0/0:7 0/0:7 0/0:5 0/0:7 0/0:10 0/0:3 0/0:8 0/0:5 0/0:3 0/0:1 0/0:1 0/0:8 0/0:3 0/0:4 0/0:7 0/0:6 0/0:2 0/0:2 0/0:1 0/0:2 0/0:5 0/0:3 0/0:9 0/0:7 0/0:6 0/0:2 0/0:14 0/0:3 0/0:7 0/0:9 0/0:4 0/0:3 0/0:3 0/0:3 0/0:4 0/0:3 0/0:8 0/0:11 0/0:3 0/0:7 0/0:6 0/0:4 0/0:6 0/0:3 0/0:9 0/0:2 0/0:8 0/0:6 0/0:10 0/0:5 0/0:1 0/0:4 0/0:1 0/0:4 0/0:5 0/0:8 0/0:4 0/0:7 0/0:3 0/0:5 0/0:6 0/0:11 0/0:6 0/0:12 0/0:5 0/0:8 0/0:6 0/0:5 0/0:8 0/0:3 0/0:9 0/0:7 0/0:8 0/0:6 0/0:6 0/0:4 0/0:3 0/0:8 0/0:5 0/0:10 0/0:12 0/0:5

    12 50235340 . G . 29.23 . AN=240;DP=575;MQ=59.38;MQ0=0 GT:DP 0/0:3 0/0:1 0/0:5 0/0:3 0/0:4 0/0:1 0/0:6 0/0:3 0/0:3 0/0:7 0/0:9 0/0:5 0/0:5 0/0:3 0/0:5 0/0:2 0/0:4 0/0:6 0/0:7 0/0:9 0/0:4 0/0:4 0/0:5 0/0:2 0/0:4 0/0:4 0/0:1 0/0:6 0/0:2 0/0:6 0/0:4 0/0:2 0/0:2 0/0:5 0/0:5 0/0:5 0/0:2 0/0:3 0/0:10 0/0:1 0/0:1 0/0:4 0/0:3 0/0:5 0/0:3 0/0:1 0/0:6 0/0:6 0/0:10 0/0:8 0/0:4 0/0:5 0/0:1 0/0:3 0/0:4 0/0:6 0/0:6 0/0:2 0/0:6 0/0:6 0/0:4 0/0:11 0/0:1 0/0:4 0/0:5 0/0:3 0/0:3 0/0:10 0/0:3 0/0:3 0/0:7 0/0:5 0/0:6 0/0:8 0/0:4 0/0:9 0/0:6 0/0:3 0/0:10 0/0:2 0/0:9 0/0:11 0/0:8 0/0:6 0/0:4 0/0:2 0/0:2 0/0:6 0/0:10 0/0:2 0/0:9 0/0:6 0/0:4 0/0:6 0/0:4 0/0:8 0/0:1 0/0:6 0/0:2 0/0:7 0/0:2 0/0:7 0/0:4 0/0:3 0/0:4 0/0:5 0/0:3 0/0:7 0/0:4 0/0:3 0/0:6 0/0:2 0/0:3 0/0:7 0/0:5 0/0:11 0/0:6 0/0:10 0/0:1 0/0:4

    Any thoughts on what is causing the error message and how to avoid it? Thanks.

    Post edited by tommycarstensen on
  • tommycarstensentommycarstensen Posts: 49Member

    Please ignore my comment. I had only regenerated 3 of my 4 VCFs. The regeneration of the 4th one fixed the problem. I'm not sure, why the VCF file was malformed in the first place and I can't see that it is malformed. I recently ran out of disk space. It might be related to this. Sorry for posting.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,210Administrator, GSA Member admin

    No worries, just glad it's resolved.

    If you ran out of space maybe the file was truncated.

    Geraldine Van der Auwera, PhD

  • tommycarstensentommycarstensen Posts: 49Member

    The thing that puzzled me was that I had the expected number of columns in all 4 lines and it was not the last line of the file in any of the 4 VCF files. However, problem resolved and it most probably originated at my end. Thank you.

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