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samtools

Tools for handling high-throughput sequencing (genomics) data. tldr-pages

On several platforms

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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 --bam input.sam >output.bamIdentify

Take input from stdin (-) and print the SAM header and any reads overlapping a specific region to stdout

other_command | samtools view --with-header - chromosome:start-endIdentify

Sort file and save to BAM (the output format is automatically determined from the output file's extension)

samtools sort input --output output.bamIdentify

Index a sorted BAM file (creates sorted_input.bam.bai)

samtools index sorted_input.bamIdentify

Print alignment statistics about a file

samtools flagstat sorted_inputIdentify

Count alignments to each index (chromosome/contig)

samtools idxstats sorted_indexed_inputIdentify

Merge multiple files

samtools merge output input1 input2 ...Identify

Split input file according to read groups

samtools split merged_inputIdentify