Annotation of SNPs

[Magnus Jespersen]

I'm trying to compare some genomes of Listeria to identify SNPs. My problem is that I cannot get kSNP to annotate the SNPs identified. I have tried the following commands:

$ kSNP3 -in in_file.txt -outdir results_20 -k 20 -CPU 4 -vcf -annotate annotation_genome.txt -all_annotations

$ kSNP3 -in in_file.txt -outdir results_20 -k 20 -CPU 4 -vcf -annotate annotation_genome.txt -genbank GCF_0001960351_ASM19603v1_genomic.gbff

The in_file contains 9 fasta files containing the raw reads of my strains and a reference fasta file downloaded from NCBI.
The annotation_genome.txt holds the name of the reference genome from the in_file.txt.
The file given to the -genbank argument is an annotated genbank file for the Ref genome.

When the results comes out there is no annotation, but only "Not in annotated genome".
Do I miss something or is there a reason that kSNP does not annotate the SNPs idenfiied?

[Barry G. Hall]

Be sure you are using kSNP v 3.1, the latest version. After NCBI discontinued use of GI numbers annotation would not work at all with earlier versions. The -genbank option doesn’t work at all.

See the attached Troubleshooting file.

Barry G. Hall

On May 14, 2018, at 2:35 AM, Magnus Jespersen magnusjespersen@users.sourceforge.net wrote:

I'm trying to compare some genomes of Listeria to identify SNPs. My problem is that I cannot get kSNP to annotate the SNPs identified. I have tried the following commands:

$ kSNP3 -in in_file.txt -outdir results_20 -k 20 -CPU 4 -vcf -annotate annotation_genome.txt -all_annotations

$ kSNP3 -in in_file.txt -outdir results_20 -k 20 -CPU 4 -vcf -annotate annotation_genome.txt -genbank GCF_0001960351_ASM19603v1_genomic.gbff

The in_file contains 9 fasta files containing the raw reads of my strains and a reference fasta file downloaded from NCBI.
The annotation_genome.txt holds the name of the reference genome from the in_file.txt.
The file given to the -genbank argument is an annotated genbank file for the Ref genome.

When the results comes out there is no annotation, but only "Not in annotated genome".
Do I miss something or is there a reason that kSNP does not annotate the SNPs idenfiied?

Annotation of SNPs https://sourceforge.net/p/ksnp/discussion/general/thread/d4b4d123/?limit=25#742a
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