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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.
samtools view -S -b {input.sam} > {output.bam}
{other_command} | samtools view -h - chromosome:start-end
samtools sort {input} -o {output.bam}
samtools index {sorted_input.bam}
samtools flagstat {sorted_input}
samtools idxstats {sorted_indexed_input}
samtools merge {output} {input1 input2 …}
samtools split {merged_input}
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