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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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