reporting lots of warnings and errors by SnpEff
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?
1 answer
look at the output of snpeff on stderr, warning are often small things like "transcript without known stop codon"
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Pierre Lindenbaum
Is the reason for these warnings is unknown start/stop codon or incomplete transcript?
yes it's quite common.
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Pierre Lindenbaum
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