New answers tagged samtools
3
votes
Problem with samtools command with a final hyphen
The hyphen "-" character is commonly used as a placeholder in Unix commands to represent the standard input (stdin) or standard output (stdout) streams. From the POSIX specification:
...
- 2,481
3
votes
Accepted
Problem with samtools command with a final hyphen
It allows you to chain commands together to avoid creating intermediate files and simplify your workflow:
Samtools is designed to work on a stream. It regards an input file `-'
as the standard input (...
- 1,434
2
votes
Accepted
Nextflow Error: failed to read header from "-"
This is not a Nextflow error. The problem is that without an input file, samtools sort tries to read from stdin. Using a recent ...
- 2,481
2
votes
Extracting all reads from bam file which match read IDs in another file
samtools can do this natively too using -N, --qname-file CLI option:
...
- 121
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