back to context overview

samtools

List of commands for samtools:

- samtools
samtools:tldr:0f0c3 samtools: Split input file according to read groups.

$ samtools split ${merged_input}

try on your machine

explain this command
- samtools
samtools:tldr:14572 samtools: Merge multiple files.

$ samtools merge ${output} ${input1 input2 …}

try on your machine

explain this command
- samtools
samtools:tldr:21f3a samtools: Print alignment statistics about a file.

$ samtools flagstat ${sorted_input}

try on your machine

explain this command
- samtools
samtools:tldr:50b74 samtools: Count alignments to each index (chromosome / contig).

$ samtools idxstats ${sorted_indexed_input}

try on your machine

explain this command
- samtools
samtools:tldr:8b455 samtools: Sort file and save to BAM (the output format is automatically determined from the output file's extension).

$ samtools sort ${input} -o ${output-bam}

try on your machine

explain this command
- samtools
samtools:tldr:9a477 samtools: Index a sorted BAM file (creates {{sorted_input.bam.bai}}).

$ samtools index ${sorted_input-bam}

try on your machine

explain this command
- samtools
samtools:tldr:daa86 samtools: Convert a SAM input file to BAM stream and save to file.

$ samtools view -S -b ${input-sam} > ${output-bam}

try on your machine

explain this command

back to context overview