samtools-samples - Man Page

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

-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 reference file.

-F FILE

read a file containing the paths to indexed fasta files. One path per line.

-X

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.

  $  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

• print wether 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

• 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

• 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

• 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

• 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

• provide a list of reference sequences with option '-F', print the associated 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

Written by Pierre Lindenbaum from Institut du Thorax U1087, Nantes, France.

Samtools website: <http://www.htslib.org/>