Inconsistent return of ERROR_OUT_OF_CHROMOSOME_RANGE

[danieljrichard]

Describe the issue A clear and concise description of what the issue is.

I'm trying to annotate mouse mm10 variants with SnpEff. The majority of my variants give 'ERROR_OUT_OF_CHROMOSOME_RANGE' errors (though they're well within the mm10 chromosome). But some coordinates don't give this error. And I can't tell the difference between rejected and not-rejected variants.

To Reproduce

1. SnpEff version: 5.2a
2. Genome version: mm10
3. SnpEff full command line: java -Xmx8g -jar /home/daniel/snpEff/snpEff.jar mm10 TIMECOURSE_agglomerated_mutations.vcf > TIMECOURSE_agglomerated_mutations.ann.vcf
4. Output / Error message: Please include detailed infomration, such as transcript ID, VCF line output, etc. #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT V1 1 177238928 1-177238928-177238928 A G . PASS ANN=G|intron_variant|MODIFIER|Akt3|Akt3|transcript|NM_011785.4|protein_coding|1/12|c.46+9748T>C|||||| GT:AD:DP:OTH:PL:ALL 1/1 1 0 1-88273902-88273902 C A . PASS ANN=A||MODIFIER|||||||||||||ERROR_OUT_OF_CHROMOSOME_RANGE GT:AD:DP:OTH:PL:ALL 1/1 1 0 1-88273957-88273957 C T . PASS ANN=T||MODIFIER|||||||||||||ERROR_OUT_OF_CHROMOSOME_RANGE GT:AD:DP:OTH:PL:ALL 1/1 1 0 1-88274858-88274858 G T . PASS ANN=T||MODIFIER|||||||||||||ERROR_OUT_OF_CHROMOSOME_RANGE GT:AD:DP:OTH:PL:ALL 1/1 12 0 12-88722875-88722875 C G . PASS ANN=G||MODIFIER|||||||||||||ERROR_OUT_OF_CHROMOSOME_RANGE GT:AD:DP:OTH:PL:ALL 1/1 14 0 14-24494054-24494054 A G . PASS ANN=G||MODIFIER|||||||||||||ERROR_OUT_OF_CHROMOSOME_RANGE GT:AD:DP:OTH:PL:ALL 1/1 15 0 15-98931668-98931668 C A . PASS ANN=A||MODIFIER|||||||||||||ERROR_OUT_OF_CHROMOSOME_RANGE GT:AD:DP:OTH:PL:ALL 1/1 16 0 16-43508924-43508924 T C . PASS ANN=C||MODIFIER|||||||||||||ERROR_OUT_OF_CHROMOSOME_RANGE GT:AD:DP:OTH:PL:ALL 1/1 17 0 17-44107174-44107174 C G . PASS ANN=G||MODIFIER|||||||||||||ERROR_OUT_OF_CHROMOSOME_RANGE GT:AD:DP:OTH:PL:ALL 1/1 6 127151008 6-127151008-127151008 G C . PASS ANN=C|5_prime_UTR_variant|MODIFIER|Ccnd2|Ccnd2|transcript|NM_009829.3|protein_coding|1/5|c.-235C>G|||||235|,C|intron_variant|MODIFIER|9330179D12Rik|9330179D12Rik|transcript|NR_040273.1|pseudogene|1/2|n.193+1190G>C||||||,C|intron_variant|MODIFIER|9330179D12Rik|9330179D12Rik|transcript|NR_040274.1|pseudogene|1/2|n.175+1445G>C||||||,C|intron_variant|MODIFIER|9330179D12Rik|9330179D12Rik|transcript|NR_040275.1|pseudogene|1/1|n.193+1190G>C|||||| GT:AD:DP:OTH:PL:ALL 1/1 9 0 9-57484620-57484620 G A . PASS ANN=A||MODIFIER|||||||||||||ERROR_OUT_OF_CHROMOSOME_RANGE GT:AD:DP:OTH:PL:ALL 1/1

Expected behavior A clear and concise description of what you expected to happen (show program's output for comparisson)

Data

##fileformat=VCFv4.2 ##source=cellSNP_v1.2.3 ##FILTER=<ID=PASS,Description="All filters passed"> ##FILTER=<ID=.,Description="Filter info not available"> ##contig=<ID=1> ##contig=<ID=2> ##contig=<ID=3> ##contig=<ID=4> ##contig=<ID=5> ##contig=<ID=6> ##contig=<ID=7> ##contig=<ID=8> ##contig=<ID=9> ##contig=<ID=10> ##contig=<ID=11> ##contig=<ID=12> ##contig=<ID=13> ##contig=<ID=14> ##contig=<ID=15> ##contig=<ID=16> ##contig=<ID=17> ##contig=<ID=18> ##contig=<ID=19> ##contig=<ID=20> ##contig=<ID=21> ##contig=<ID=22> ##contig=<ID=X> ##contig=<ID=Y> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT V1 1 177238928 1-177238928-177238928 A G . PASS . GT:AD:DP:OTH:PL:ALL 1/1 1 88273902 1-88273902-88273902 C A . PASS . GT:AD:DP:OTH:PL:ALL 1/1 1 88273957 1-88273957-88273957 C T . PASS . GT:AD:DP:OTH:PL:ALL 1/1 1 88274858 1-88274858-88274858 G T . PASS . GT:AD:DP:OTH:PL:ALL 1/1 12 88722875 12-88722875-88722875 C G . PASS . GT:AD:DP:OTH:PL:ALL 1/1

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