Print Sam Header And Reads

Prints the header and specific read segments from a SAM file based on provided parameters.

Terminal

<other_command> | samtools view -h - chromosome:start-end

<other_command> | samtools view -h - chromosome:start-end

#!/bin/bash

# Print Sam Header And Reads
{{other_command}} | samtools view {{[-h|--with-header]}} - chromosome:start-end

When To Use

To examine the header information and alignments of specific genomic regions in a SAM file.

Pro Tip

Filter the output using pipe commands to process reads efficiently for quality checks or filtering.

Anatomy of Output

Understanding the result

@HD VN:1.0 SO:unsorted Header Info

SAM header line with version and sorting order.

chr1 1001 0 60 42 5S40M Read Info

A single read alignment with chromosome position and quality.

# 2 sequences read. Summary

Indicating the number of sequences retrieved.

Troubleshooting

Error: Unknown chromosome 'unknown_chr'.

Solution: Ensure the chromosome name exists in the reference genome.

Error: Invalid range specified: start >= end.

Solution: Check start and end positions, ensuring start is less than end.

Error: Input SAM file not found.

Solution: Verify the path of the specified SAM file.

Command Breakdown

<other_command>: Base Command; The executable that performs this operation. Here it runs Other Command before the shell applies any redirect operators.
<other_command>: other command; The value supplied for other command.
-h: h| with header; The value supplied for h| with header.
-h: Command Option; Tool-specific option used by this command invocation.
-: Command Option; Tool-specific option used by this command invocation.

Alternative Approaches

Alternative data processing tools for the same job.