use of --snp_dist argument #282
Replies: 1 comment
-
i got it |
Beta Was this translation helpful? Give feedback.
0 replies
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
-
Hi @jodyphelan
Please i would like to know where i should put the --snp_dist agrument.
I wrote my command like that
tb-profiler profile -1 /home/justicengom/fastqs/R27406_R1.fastq.gz -2 /home/justicengom/fastqs/R27406_R2.fastq.gz -p prefix --call_whole_genome --spoligotype --snp_dist
this is what appeared on my screen :
usage: tb-profiler profile [-h] [--read1 READ1] [--read2 READ2] [--bam BAM] [--fasta FASTA] [--vcf VCF] [--platform {illumina,nanopore,pacbio}] [--db DB] [--external_db EXTERNAL_DB] [--prefix PREFIX] [--csv] [--txt] [--pdf] [--output_template OUTPUT_TEMPLATE] [--add_columns ADD_COLUMNS] [--dir DIR] [--mapper {bwa,minimap2,bowtie2,bwa-mem2}] [--caller {bcftools,gatk,freebayes,pilon,lofreq}] [--calling_params CALLING_PARAMS] [--min_depth MIN_DEPTH] [--af AF] [--reporting_af REPORTING_AF] [--coverage_fraction_threshold COVERAGE_FRACTION_THRESHOLD] [--missing_cov_threshold MISSING_COV_THRESHOLD] [--suspect] [--spoligotype] [--call_whole_genome] [--snp_dist SNP_DIST] [--no_trim] [--no_flagstat] [--no_clip] [--no_delly] [--threads THREADS] [--ram RAM] [--verbose {0,1,2}] [--temp TEMP] [--version] tb-profiler profile: error: argument --snp_dist: expected one argument
thank you
Beta Was this translation helpful? Give feedback.
All reactions