2
votes
Accepted
Bacterial genomes and snpeff warnings 'WARNING_TRANSCRIPT_NO_START_CODON'
Bacteria have a different translation table from eukaryote nuclear DNA; it may be that SnpEff is expecting human genes in the genome. Have you followed the build steps outlined in the documentation?
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- 14.1k
2
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which SNP effect software, such as VEP, annovar or snpEff, allows the user to submit their own annotations in gtf format?
All of them have ways you can add your own annotation dataset but I've found the easiest way to be to use bcftools annotate. You can give it a tab-delimited (GTF is tab-delimited, but might need some ...
- 2,311
1
vote
Bacterial genomes and snpeff warnings 'WARNING_TRANSCRIPT_NO_START_CODON'
According to your report, you are using human HG18 as the reference genome version. Therefore, the report will be wrong along with the wrong codons warnings. It is unfruitful to try with a human ...
- 11
1
vote
Questions regarding the detection of variants (SNPs and Indels) in mammal
This is close to what many people do. May I add:
between 4 and 5 you might want to add read groups using Picard. This will allow GATK to work. For this purpose (in case picard gives you issues), some ...
- 111
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