snpEff - ERROR_CHROMOSOME_NOT_FOUND

Question

[ar.satkhol18]

Hi, I tried to run snpEff for annotating variants with the following command:

java -Xmx4g -jar snpEff.jar GRCh37.75 -interval ~/ngs/reference.fasta ~/Desktop/somsnp.vcf > snp.ann.vcf

I am getting the following result in the output vcf file:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NORMAL  TUMOR
chr1:115247054-115248254    867 .   G   T   .   PASS    DP=7199;GPV=1E0;SOMATIC;SPV=7.0825E-15;SS=2;SSC=141;ANN=T||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND  GT:AD:DP:DP4:FREQ:RD    0/0:0:7160:6403,743,0,0:0%:7146 0/1:6:39:11,17,1,5:17.65%:28
chr1:115248392-115250893    1583    .   C   T   .   PASS    DP=5912;GPV=1E0;SOMATIC;SPV=5.2216E-9;SS=2;SSC=82;ANN=T||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND    GT:AD:DP:DP4:FREQ:RD    0/0:1:5876:4230,1619,1,0:0.02%:5849 0/1:4:36:24,7,1,3:11.43%:31
chr2:209100921-209101921    279 .   T   C   .   PASS    DP=6817;GPV=1E0;SOMATIC;SPV=5.4401E-4;SS=2;SSC=32;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND    GT:AD:DP:DP4:FREQ:RD    0/0:485:6741:5044,1189,460,25:7.22%:6233    0/1:14:76:41,16,12,2:19.72%:57

The reference file used for alignment and variant calling is a fasta file extracted from hg19 genome sequence with custom bed file using bedtools getfasta. Please help me with this error

[WouterDeCoster]

Where is the error?

The reference file used for alignment and variant calling is a fasta file extracted from hg19 genome sequence with custom bed file using bedtools getfasta.

That is not recommended. You should align against the full genome.

[ar.satkhol18]

Ok. I'll try that. Thank you The error is under the TUMOR column at the far right

[Kevin Blighe]

You may have different contig names between your VCF and annotation, e.g., "chr1" versus just "1"

[WouterDeCoster]

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