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Hello,
I used samtools mpileup and ivar variants to identify codon and amino acid changes in assembled genomes with reference genome and .gff3 files. It turned out the codon and amino acid listed in the .tsv file don't match the actual codon and amino acid in reference CDS and protein fasta files.
Below is the command I used:
mpi_cmd_str = f'samtools mpileup -aa -A -d 20000 -B -Q 0 {sample}.sorted.bam '
ivar_cmd_str = f'ivar variants -p mutations -q 30 -t 0.03 -r {ref_file} -g {gff_file}'
cmd_str = mpi_cmd_str + " | " + ivar_cmd_str
os.system(cmd_str)
As an example, in the excel screenshot below you can find the sequence validation for SARS-CoV-2 ORF1ab.
Any suggestion?
Thank you very much!
The text was updated successfully, but these errors were encountered:
Hello,
I used samtools mpileup and ivar variants to identify codon and amino acid changes in assembled genomes with reference genome and .gff3 files. It turned out the codon and amino acid listed in the .tsv file don't match the actual codon and amino acid in reference CDS and protein fasta files.
Below is the command I used:
mpi_cmd_str = f'samtools mpileup -aa -A -d 20000 -B -Q 0 {sample}.sorted.bam '
ivar_cmd_str = f'ivar variants -p mutations -q 30 -t 0.03 -r {ref_file} -g {gff_file}'
cmd_str = mpi_cmd_str + " | " + ivar_cmd_str
os.system(cmd_str)
As an example, in the excel screenshot below you can find the sequence validation for SARS-CoV-2 ORF1ab.
![screenshot](https://private-user-images.githubusercontent.com/112007035/296900528-9efa3e46-18ab-48e9-aabc-ede614403bb0.jpg?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjYwNzUwNzcsIm5iZiI6MTcyNjA3NDc3NywicGF0aCI6Ii8xMTIwMDcwMzUvMjk2OTAwNTI4LTllZmEzZTQ2LTE4YWItNDhlOS1hYWJjLWVkZTYxNDQwM2JiMC5qcGc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwOTExJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDkxMVQxNzEyNTdaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT1kNmYyZjFlNzBiODc3NjNjZTk3OTYyNWMzZTdmOTkxNDkyYTMzNDgzYzE0YjhiMzRkMTM5MWM0NTNhYWRkNmMwJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.vqIpWN4HvqI3k_AcysSjQEQHPdxdShIs-_3s_xyD0Mo)
Any suggestion?
Thank you very much!
The text was updated successfully, but these errors were encountered: