Samtools does not retrieve the entire alignment file unless Samtools is also able to open a BAM (not SAM) file on a remote FTP or HTTP server if the BAM file name starts with 'ftp://' or ' SamtoolsĬhecks the current working directory for the index file and will download the index upon absence. Samtools always output warning and error messages to the standard error output (stderr). Several commands can thus be combined with Unix pipes. It regards an input file '-' as the standard input (stdin) and an output file '-' as the standard output (stdout). Samtools is designed to work on a stream. Sorting, merging and indexing, and allows to retrieve reads in any regions swiftly. It imports from and exports to the SAM (Sequence Alignment/Map) format, does Samtools is a set of utilities that manipulate alignments in the BAM format. Samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bamīcftools view in.bcf chr2:100-200 > out.vcfīcftools view -vc in.bcf > out.vcf 2> out.afs Samtools merge out.bam in1.bam in2.bam in3.bam Samtools view -bt ref_list.txt -o aln.bam
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