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
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