reporting lots of warnings and errors by SnpEff
1
1
Entering edit mode
23 months ago
Alireza ▴ 30

Hi all.

I ran the GATK germline short variant discovery pipeline on my samples.

My samples are related to dog organisms, and I aligned the sample read with canFam3 using BWA.

canFam3: https://genome.ucsc.edu/cgi-bin/hgGateway?db=canFam3

but after annotating variants using SnpEff (I selected CanFam3 as SnpEff db), lots of warnings and some errors has been reported.

enter image description here

What does it mean?

does it necessary to build my own db?

NGS SnpEff WGS Annotating WES • 1.2k views
ADD COMMENT
1
Entering edit mode
23 months ago

look at the output of snpeff on stderr, warning are often small things like "transcript without known stop codon"

ADD COMMENT
0
Entering edit mode

the warnings are: WARNING_TRANSCRIPT_NO_START_CODON number: 34801 WARNING_TRANSCRIPT_NO_STOP_CODON number: 8796 WARNING_TRANSCRIPT_INCOMPLETE number: 9

ADD REPLY
0
Entering edit mode

Is it ok? Is the reason for these warnings is unknown start/stop codon or incomplete transcript?

ADD REPLY
0
Entering edit mode

Is the reason for these warnings is unknown start/stop codon or incomplete transcript?

yes it's quite common.

ADD REPLY
0
Entering edit mode

many thanks Pierre

ADD REPLY

Login before adding your answer.

Traffic: 1337 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6