Hello all,
I am trying to annotate VCF files using snpEff. I'm using a virus that doesn't have good gene annotations available so I had to build a custom database. That seemed to work well but when I actually try to do the annotation I'm not getting the amino acid changes called. Here is the output
The problem seems to be java.lang.NullPointerException. However, I'm not sure what this means.
I have tried using different variant callers (lofreq and callvariants.sh). I have also tried annotating both a .gbk and a .gff3 file with the same result.
Any thoughts?
I am trying to annotate VCF files using snpEff. I'm using a virus that doesn't have good gene annotations available so I had to build a custom database. That seemed to work well but when I actually try to do the annotation I'm not getting the amino acid changes called. Here is the output
Code:
weger@IDANGS01:~/snpEff$ java -jar snpEff.jar dengue_DR59_2 /data/ebel_lab/Weger/Experiment_27/36_Exp/test/323-minority.vcf > 323-minority_ann.vcf -noGenome Error: Error while processing VCF entry (line 59) : gb:AB122022|Organism:Dengue 3152 . C CA 36.83 PASS SN=0;STA=3152;STO=3152;TYP=INS;R1P=198;R1M=195;R2P=0;R2M=0;PPC=0;LS=54650;MQS=15536;MQM=42;BQS=13814;BQM=36;EDS=15658;EDM=75;IDS=385516;IDM=992;COV=18847;MCOV=-1;CED=601;HMP=0;DP=18847;AF=0.0209;RAF=0.0209;SB=1.0000;DP4=9226,9228,198,195 GT:DP:AD:AF:RAF:SB:SC:PF 1:18847:393:0.0209:0.0209:1.0000:36.83:PASS java.lang.NullPointerException Error: Error while processing VCF entry (line 65) : gb:AB122022|Organism:Dengue 5915 . C CA 37.11 PASS SN=0;STA=5915;STO=5915;TYP=INS;R1P=228;R1M=211;R2P=0;R2M=0;PPC=0;LS=61291;MQS=17579;MQM=42;BQS=15431;BQM=36;EDS=16893;EDM=75;IDS=431762;IDM=992;COV=7479;MCOV=-1;CED=601;HMP=0;DP=7479;AF=0.0587;RAF=0.0587;SB=0.9999;DP4=3512,3528,228,211 GT:DP:AD:AF:RAF:SB:SC:PF 1:7479:439:0.0587:0.0587:0.9999:37.11:PASS java.lang.NullPointerException Error: Error while processing VCF entry (line 75) : gb:AB122022|Organism:Dengue 8469 . C CA 36.46 PASS SN=0;STA=8469;STO=8469;TYP=INS;R1P=59;R1M=56;R2P=0;R2M=0;PPC=0;LS=16215;MQS=4113;MQM=41;BQS=4059;BQM=36;EDS=5218;EDM=75;IDS=111026;IDM=992;COV=5471;MCOV=-1;CED=601;HMP=0;DP=5471;AF=0.0210;RAF=0.0210;SB=0.9999;DP4=2677,2679,59,56 GT:DP:AD:AF:RAF:SB:SC:PF 1:5471:115:0.0210:0.0210:0.9999:36.46:PASS java.lang.NullPointerException 3 errors.
I have tried using different variant callers (lofreq and callvariants.sh). I have also tried annotating both a .gbk and a .gff3 file with the same result.
Any thoughts?
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