SNP annotation from RNA-seq data without referene

Question

[paraskevopou]

Dear all! I have a vcf file with SNPs among two individuals and I would like to annotate those SNPs. vcf file looks like the following

TRINITY_DN9255_c0_g1    226 .   C   A   5762.77 PASS    .   GT:AD:DP:GQ:PL  1/1:0,146:146:99:5791,459,0
TRINITY_DN9573_c0_g1    51  .   A   C   6742.77 PASS    .   GT:AD:DP:GQ:PL  1/1:0,204:204:99:6771,610,0
TRINITY_DN9573_c0_g1    313 .   G   C   9761.77 PASS    .   GT:AD:DP:GQ:PL  1/1:1,287:288:99:9790,857,0
TRINITY_DN10141_c1_g1   1018    .   G   A   5078.77 PASS    .   GT:AD:DP:GQ:PL  1/1:0,146:146:99:5107,435,0
TRINITY_DN13710_c0_g1   495 .   T   A   43.28   PASS    .   GT:AD:DP:GQ:PL  1/1:0,3:3:9:71,9,0
TRINITY_DN13710_c0_g1   533 .   G   A   62.28   PASS    .   GT:AD:DP:GQ:PL  1/1:0,3:3:9:90,9,0
TRINITY_DN23295_c0_g1   303 .   T   C   184.84  PASS    .   GT:AD:DP:GQ:PL  1/1:0,6:6:18:213,18,0

I tried to use SnpEff to annotate my SNPs according to a close related genome but what I get at the ANN field is

ANN=A||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND

My transcriptome is de novo assembly. And for calling SNPs i used the supertranscript pipeline on trinity.

Here is the command I used

java -Xmx4g -jar snpEff.jar Helobdella_robusta SNPs.vcf > SNPs.ann.vcf

Do you have any idea how should I proceed? Any helpful would be useful. Thanks a lot in advance Sofia

Answer 1

[d-cameron]

SnpEff needs a database to perform genomic annotations. Since you are using a custom reference genome (your de novo assembly), you need to supply SnpEff with the reference data it requires (such as gene annotation so it can work out whether a SNP changes a protein).

I highly recommend reading the relevant documentation at the following URL: http://snpeff.sourceforge.net/SnpEff_manual.html#databases