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> Tools for handling high-throughput sequencing (genomics) data.
> Used for reading/writing/editing/indexing/viewing of data in SAM/BAM/CRAM format.
Convert a SAM input file to BAM stream and save to file:
samtools view -S -b {input.sam} > {output.bam}
Take input from stdin (-) and print the SAM header and any reads overlapping a specific region to stdout:
{other_command} | samtools view -h - chromosome:start-end
Sort file and save to BAM (the output format is automatically determined from the output file's extension):
samtools sort {input} -o {output.bam}
Index a sorted BAM file (creates {sorted_input.bam.bai}):
samtools index {sorted_input.bam}
Print alignment statistics about a file:
samtools flagstat {sorted_input}
Count alignments to each index (chromosome / contig):
samtools idxstats {sorted_indexed_input}
Merge multiple files:
samtools merge {output} {input1 input2 …}
Split input file according to read groups:
samtools split {merged_input}
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> This work is licensed under the Creative Commons Attribution 4.0 International License (CC-BY).
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