reporting lots of warnings and errors by SnpEff

Question

[Alireza]

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.

What does it mean?

does it necessary to build my own db?

Answer 1

[Pierre Lindenbaum]

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

[Alireza]

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

[Alireza]

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

[Pierre Lindenbaum]

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

yes it's quite common.

[Alireza]

many thanks Pierre