ngs-fzb / binosnp Goto Github PK
View Code? Open in Web Editor NEW:mag: :pill: Detection of low-frequency SNPs in next-generation sequencing data of Mycobacterium tuberculosis complex strains
License: GNU General Public License v3.0
:mag: :pill: Detection of low-frequency SNPs in next-generation sequencing data of Mycobacterium tuberculosis complex strains
License: GNU General Public License v3.0
Hi, I have a problem when running the script, it does not detect the *.bam file. This is the terminal output:
./binoSNP ./GATK_Bam/*.bam
[2022-04-14 00:45:33] Processing ./GATK_Bam/sequence_01.gatk.bam
[2022-04-14 00:45:33] Starting bam-readcount
[2022-04-14 00:45:33] bam-readcount ./GATK_Bam/sequence_01.gatk.bam -b 20 -w 0 -f /home/.../binoSNP/var/M._tuberculosis_H37Rv_2015-11-13.fasta -l /home/.../binoSNP/var/Resisnps_Master.v28.interval_list.tsv > Low_Freq/sequence_01.gatk.txt
sh: 1: bam-readcount: not found
[2022-04-14 00:45:33] bam-readcount ./GATK_Bam/sequence_01.gatk.bam -b 20 -w 0 -f /home/.../binoSNP/var/M._tuberculosis_H37Rv_2015-11-13.fasta -l /home/.../binoSNP/var/Resisnps_Master.v28.interval_list.tsv > Low_Freq/sequence_01.gatk.txt did not work: 32512
What do you think is the problem?
best regards
Ricardo
I don't have system perl, mine is in a different location
This will ensure the first one in PATH is used.
http://www.github.de/ngs-fzb/binoSNP is in the paper
www.github.de's server IP address could not be found.
Hi there,
I'd like to use binoSNP
to detect subpopulations in my eukaryotic RNA-seq data and tried to set it up accordingly by supplying my own list of intervals, mutation table and (multiple scaffold/chromosome) reference sequence.
Although binoSNP
appears to run smoothly on the supplied files, the output is empty.
I'm currently don't know where the issue is but wondered if you could provide an example bam.file
to test that binoSNP runs smoothly in my environment?
Also, I'd appreciate any tips on how to use binoSNP
on eukaryotic data sets.
Many thanks in advance for your help!
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