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samtools-samples(1) Bioinformatics tools samtools-samples(1) NAME samtools samples - prints the samples from an alignment file SYNOPSIS samtools samples [options] (<input>|stdin) samtools samples [options] -X f1.bam f2.bam ... f1.bam.bai f2.bam.bai ... DESCRIPTION Print the sample names found in the read-groups and the path to the refer- ence genome from alignment files. The output of this tool can be used to create an input for any popular workflow manager. The input is a list of SAM/BAM/CRAM files, or the path to those files can be provided via stdin. The output is tab-delimited containing the sample name as the first column, the path to the alignment file as the second column, the path to the refer- ence genome as a third optional column and a single character flag (Y/N) indicating whether the alignment file is indexed or not as a fourth op- tional column. If no reference is found for an alignment, a dot (.) will be used in the reference path column. If no sample is available in any read-group header, a dot (.) will be used as the sample name. If a BAM file contains more than one sample, one line will be printed for each sample. OPTIONS -? print help and exit -h print a header -i test if the file is indexed. Add an extra column to the output with a single character value (Y/N). -T TAG provide the sample tag name from the @RG line [SM]. -o FILE output file [stdout]. -f FILE load an indexed fasta file in the collection of references. Can be used multiple times. Add an extra column with the path to the ref- erence file. -F FILE read a file containing the paths to indexed fasta files. One path per line. -X use a custom index file. EXAMPLES o print the samples from a set of BAM/SAM files, with a header. There is no sample defined in the header of 'example.sam', so a dot is used for the sample name. $ samtools samples -h S*.bam *.sam #SM PATH S1 S1.bam S2 S2.bam S3 S3.bam S4 S4.bam S5 S5.bam . example.sam o print the samples from a set of BAM/SAM files, with a header, print whether the file is indexed. $ samtools samples -i -h S*.bam *.sam #SM PATH INDEX S1 S1.bam Y S2 S2.bam Y S3 S3.bam Y S4 S4.bam Y S5 S5.bam Y . example.sam N o print whether the files are indexed using custom bai files. $ samtools samples -i -h -X S1.bam S2.bam S1.bam.bai S2.bam.bai #SM PATH INDEX S1 S1.bam Y S2 S2.bam Y o read a tab delimited input <file>(tab)<bai> and print whether the files are indexed using custom bai files. $ find . -type f \( -name "S*.bam" -o -name "S*.bai" \) | sort | paste - - | samtools samples -i -h -X #SM PATH INDEX S1 ./S1.bam Y S2 ./S2.bam Y S3 ./S3.bam Y S4 ./S4.bam Y S5 ./S5.bam Y o print the samples from a set of BAM/CRAM files, with a header, use '@RG/LB' instead of '@RG/SM'. $ samtools samples -h -T LB S*.bam #LB PATH S1 S1.bam S2 S2.bam S3 S3.bam S4 S4.bam S5Lib1 S5.bam S5Lib2 S5.bam o pipe a list of BAM/CRAM files , pipe it into samtools samples. $ find . -type f \( -name "S*.bam" -o -name "*.cram" \) | samtools samples -h #SM PATH S5 ./S5.bam S2 ./S2.bam S4 ./S4.bam S3 ./S3.bam S1 ./example.cram S1 ./S1.bam o provide two reference sequences with option '-f', print the associated reference for each BAM files. $ samtools samples -h -f reference.fa -f example.fa S*.bam *.sam *.cram #SM PATH REFERENCE S1 S1.bam reference.fa S2 S2.bam reference.fa S3 S3.bam reference.fa S4 S4.bam reference.fa S5 S5.bam reference.fa . example.sam example.fa S1 example.cram example.fa o provide a list of reference sequences with option '-F', print the associ- ated reference for each BAM files. $ cat references.list reference.fa example.fa $ samtools samples -h -F references.list S*.bam *.sam *.cram #SM PATH REFERENCE S1 S1.bam reference.fa S2 S2.bam reference.fa S3 S3.bam reference.fa S4 S4.bam reference.fa S5 S5.bam reference.fa . example.sam example.fa S1 example.cram example.fa AUTHOR Written by Pierre Lindenbaum from Institut du Thorax U1087, Nantes, France. Samtools website: <http://www.htslib.org/> samtools-1.23.1 18 March 2026 samtools-samples(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXAMPLES | AUTHOR
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