reporting lots of warnings and errors by SnpEff
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16 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 • 968 views
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16 months ago

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

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

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

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

yes it's quite common.

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many thanks Pierre

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