breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
Description: gdtools ANNOTATE in TABLE format puts an extra comma in the header after the "type" column name. Consequently, genome names and their corresponding mutations are misaligned. The header row contains:
"type",,"seq_id","position","mutation", ... input.gd file names
Expectation: The header row should contain
"type","seq_id","position","mutation", ... input.gd file names
Version: 0.38.1
Command executed:
gdtools ANNOTATE -r $REF -f TABLE -o output-file-name.tsv */output/*.gdDescription: gdtools ANNOTATE in TABLE format puts an extra comma in the header after the "type" column name. Consequently, genome names and their corresponding mutations are misaligned. The header row contains: "type",,"seq_id","position","mutation", ... input.gd file names
Expectation: The header row should contain "type","seq_id","position","mutation", ... input.gd file names
Workaround: delete the extra comma after "type"