samtools samples [options] (<input>|stdin)
samtools samples [options] -X f1.bam f2.bam ... f1.bam.bai f2.bam.bai ...
Print the sample names found in the read-groups and the path to the reference 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 reference 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 optional 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.
print help and exit
print a header
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 reference file.
- -F FILE
read a file containing the paths to indexed fasta files. One path per line.
use a custom index file.
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
print the samples from a set of BAM/SAM files, with a header, print whether the file is indexed.
print wether the files are indexed using custom bai files.
read a tab delimited input <file>(tab)<bai> and print whether the files are indexed using custom bai files.
print the samples from a set of BAM/CRAM files, with a header, use '@RG/LB' instead of '@RG/SM'.
pipe a list of BAM/CRAM files , pipe it into samtools samples.
provide two reference sequences with option '-f', print the associated reference for each BAM files.
provide a list of reference sequences with option '-F', print the associated reference for each BAM files.
Written by Pierre Lindenbaum from Institut du Thorax U1087, Nantes, France.
Samtools website: <http://www.htslib.org/>