CDS_lenght in SnpEff output is missed

Question

[paumarc]

Hi Folks

I am running snpeff annotate some mouse mutations. One of my objetives is get the CDS length to determinate the annot ation of main transcript for each gene

i just used different databases in snpeff (GRCm38.75 , GRCm38.99 and GRCm39.10) but no information was found at the cds_length file

i used the following command

java -Xmx8g -jar snpEff.jar GRCm39.105 some.vcf > out.ann.vcf

nevertheless, the possision 13 (starting with 1 at the 1srt position) corresponding to CDS.pos / CDS.length is empty (i paste an example)

##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p |
 cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
#CHROM      POS   ID    REF   ALT   QUAL  FILTER      INFO  FORMAT      21_68_TI1
10    3134517     .     G     A     35.48 .     AC=2;AF=1.00;AN=2;DP=1;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.00;QD=25.36;SOR=1.609;ANN=A|intergenic_region|MODIFIER|Gm48097-Gm6667|ENSMUSG000
00111625-ENSMUSG00000110787|intergenic_region|ENSMUSG00000111625-ENSMUSG00000110787|||n.3134517G>A||||||    GT:AD:DP:GQ:PGT:PID:PL:PS     1|1:0,1:1:3:1|1:3134517_G_A:45,3,0:3134517
10    3134540     .     A     G     58.32 .     AC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=34.00;QD=29.16;SOR=0.693;ANN=G|intergenic_region|MODIFIER|Gm48097-Gm6667|ENSMUSG000
00111625-ENSMUSG00000110787|intergenic_region|ENSMUSG00000111625-ENSMUSG00000110787|||n.3134540A>G||||||    GT:AD:DP:GQ:PGT:PID:PL:PS     1|1:0,2:2:6:1|1:3134517_G_A:70,6,0:3134517
10    3174589     .     AAC   A     35.6  .     AC=1;AF=0.500;AN=2;BaseQRankSum=0.875;DP=18;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=2.97;ReadPosRankSum=0.605;SOR=1.179;AN
N=A|intron_variant|MODIFIER|Gm6667|ENSMUSG00000110787|transcript|ENSMUST00000217169.2|unprocessed_pseudogene|1/2|n.88+10355_88+10356delGT|||||| GT:AD:DP:GQ:PL    0/1:9,3:12:43:43,0,194
10    3257312     .     C     G     104.84      .     AC=2;AF=1.00;AN=2;DP=3;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=34.95;SOR=1.179;ANN=G|downstream_gene_variant|MODIFIER|Gm18703|ENSMUSG0000
0111114|transcript|ENSMUST00000215318.2|processed_pseudogene||n.*3931C>G|||||3931|,G|intergenic_region|MODIFIER|Gm18703-Ppp1r14c|ENSMUSG00000111114-ENSMUSG00000040653|intergenic_region|ENSMUSG00000111114-ENSMUSG
00000040653|||n.3257312C>G||||||    GT:AD:DP:GQ:PL    1/1:0,3:3:9:118,9,0

Could you tell me if i missing some flag running snpeff that makes that this information is missed?

thanks