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37 lines
1.0 KiB
Markdown
37 lines
1.0 KiB
Markdown
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# samtools
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> Tools for handling high-throughput sequencing (genomics) data.
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> Used for reading/writing/editing/indexing/viewing of data in SAM/BAM/CRAM format.
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- Convert a SAM input file to BAM stream and save to file:
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`samtools view -S -b {{input.sam}} > {{output.bam}}`
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- Take input from stdin (-) and print the SAM header and any reads overlapping a specific region to stdout:
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`{{other_command}} | samtools view -h - chromosome:start-end`
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- Sort file and save to BAM (the output format is automatically determined from the output file's extension):
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`samtools sort {{input}} -o {{output.bam}}`
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- Index a sorted BAM file (creates {{sorted_input.bam.bai}}):
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`samtools index {{sorted_input.bam}}`
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- Print alignment statistics about a file:
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`samtools flagstat {{sorted_input}}`
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- Count alignments to each index (chromosome / contig):
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`samtools idxstats {{sorted_indexed_input}}`
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- Merge multiple files:
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`samtools merge {{output}} {{input_1}} [{{input_2}}...]`
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- Split input file according to read groups:
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`samtools split {{merged_input}}`
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