IGV Visualisation Problem
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Entering edit mode
5.7 years ago
morovatunc ▴ 540

Hi,

I wanted to see a specific frequency of mutations within an interval (through bed files). Therefore, I used snpsift annotate and snpsift filter for annotation and filtering. After repeating this event for ~500 files I wanted see them as a bundle, so I needed to use vcf-concatete to merge them in a single vcf file. But know, my problem is when I try to visualise this big bundle with IGV tools, I get this error,

Error loading features for interval: 16:17478977-17479244 htsjdk.tribble.TribbleException: Line 69: there aren't enough columns for line 16 17479124 . CAT C . alleleBias;QD;ALTC;VAFC;QUAL;GTQ SOMATIC;BRF=0.36;FR=0.2500;HP=2;HapScore=1;MGOF=11;MMLQ=28;MQ=55.96;NF=6;NR=2;PP=14;QD=4.125;SC=CATAAACACACATACACACAC;SbPval=0.29;Source=Platypus;TC=65;TCF=30;TCR=35;TR=8;WE=17479136;WS=17479114;HE=1 (we expected 9 tokens, and saw 8 ), for input source: /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/AR_250widen/AR_250widen_final_output_from_all_batches/EOPC-DE/DO10806/final.f601cf2f-081f-484d-ab0e-21a8ec8d3770.indel_dkfz.vcf.gz


I dont have any idea why this happens and what is wrong with my vcf files.

Does anyone have an idea about this problem ?

Help would be greatly appericiated.

Best regards,

Tunc.

EDIT: I added a sample of the vcf that I am trying to visualise.

Also, the error became like;

Line 69: there aren't enough columns for line 1 164840924 . TGTGGGGAG T . alleleBias;QD;VAF;QUAL;ALTT;GTQ;GTQFRT SOMATIC;BRF=0.17;FR=0.2499;HP=2;HapScore=1;MGOF=1;MMLQ=100;MQ=60.0;NF=0;NR=0;PP=5;QD=0;SC=CCTGGGAACCTGTGGGGAGCC;SbPval=1.0;Source=Platypus;TC=64;TCF=24;TCR=40;TR=0;WE=164840940;WS=164840914;HE=1 (we expected 9 tokens, and saw 8 ), for input source: /Users/morova/Google Drive/TuncProjectStep2-3/Yunus_HPC/AR_250widen/AR_250widen_final_output_from_all_batches/EOPC-DE/DO10806/final.f601cf2f-081f-484d-ab0e-21a8ec8d3770.indel_dkfz.vcf


The Subject vcf;

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  CONTROL TUMOR
1   164840924   .   TGTGGGGAG   T   .   alleleBias;QD;VAF;QUAL;ALTT;GTQ;GTQFRT  SOMATIC;BRF=0.17;FR=0.2499;HP=2;HapScore=1;MGOF=1;MMLQ=100;MQ=60.0;NF=0;NR=0;PP=5;QD=0;SC=CCTGGGAACCTGTGGGGAGCC;SbPval=1.0;Source=Platypus;TC=64;TCF=24;TCR=40;TR=0;WE=164840940;WS=164840914;HE=1
1   243862215   .   CA  C   .   badReads;QD;ALTC;VAFC;QUAL;GTQ  SOMATIC;BRF=0.25;FR=0.2499;HP=15;HapScore=2;MGOF=2;MMLQ=5;MQ=60.0;NF=6;NR=7;PP=28;QD=2.38461538462;SC=GAGGCTGGACCAAAAAAAAAA;SbPval=0.33;Source=Platypus;TC=56;TCF=21;TCR=35;TR=13;WE=243862239;WS=243862205;HE=1
2   20327814    .   CA  C   .   QD;ALTC;VAFC;QUAL;GTQ   SOMATIC;BRF=0.34;FR=0.2502;HP=17;HapScore=4;MGOF=13;MMLQ=20;MQ=57.24;NF=0;NR=7;PP=12;QD=2.14285714286;SC=ACTCTGTTTCCAAAAAAAAAA;SbPval=1.0;Source=Platypus;TC=50;TCF=15;TCR=35;TR=7;WE=20327824;WS=20327804;HE=1
2   227076637   .   TTATA   T   .   QUAL;ALTT;GTQ   SOMATIC;BRF=0.27;FR=0.2512;HP=1;HapScore=2;MGOF=0;MMLQ=27;MQ=60.0;NF=0;NR=1;PP=19;QD=30.0;SC=TATGTGTATATTATATATATA;SbPval=0.44;Source=Platypus;TC=22;TCF=10;TCR=12;TR=1;WE=227076649;WS=227076627;HE=1


Edit2: I understood why the problem happened. FORMAT column info was missing in the VCF's. SNP sift somehow deleted it.

Snpsift omitted that information during annotation and filtration step. Is there any idea how can I obtain that information?

Best,

Tunc.

IGV VCF snpsift vcftools • 2.2k views
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Entering edit mode

Look up that line in your file (with e.g. grep) and have a look at how it differs from other lines. Alternatively/additionally, try to delete the line (with e.g. grep -v) and see if there are more problematic lines.

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Thank you for the effort!. I somehow solved the problem. But now I have another error(I posted right below the previous one), keeps coming even If I delete the problematic line that causes problem.

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5.7 years ago
Dan D 7.3k

The error message is pretty clear. It looks like there isn't an entry for the first column (CHROM).

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Entering edit mode

Thank you for your help! I shared a sample of the vcf that I am trying to visualise. Also, the error that have been trying to fix changed and a new one came up.

But I have already got the chromosome information in my vcf so I dont think that is the case. I tried to match all the headers with the information in a single line. They are also complementing each other.

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