Software Usage Function
samtools calmd samtools calmd [-Eeubr] [-C capQcoef] <aln.bam> <ref.fasta> Generate the MD tag. If the MD tag is already present, this command will give a warning if the MD tag generated is different from the existing tag. Calmd can also read and write CRAM files although in most cases it is pointless as CRAM recalculates MD and NM tags on the fly. The one exception to this case is where both input and output CRAM files have been / are being created with the no_ref option.
java -jar picard.jar java -jar picard.jar CollectWgsMetrics I=input.bam O=collect_wgs_metrics.txt R=reference_sequence.fasta Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.
java -jar picard.jar java -jar picard.jar UpdateVcfSequenceDictionary Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.
samtools idxstats samtools idxstats aln.sorted.bam Retrieve and print stats in the index file corresponding to the input file. Before calling idxstats, the input BAM file must be indexed by samtools index.
java -jar picard.jar java -jar picard.jar CollectBaseDistributionByCycle CHART=collect_base_dist_by_cycle.pdf I=input.bam O=output.txt Chart the nucleotide distribution per cycle in a SAM or BAM fileThis tool produces a chart of the nucleotide distribution per cycle in a SAM or BAM file in order to enable assessment of systematic errors at specific positions in the reads.
samtools depth samtools depth [options] [in1.sam|in1.bam|in1.cram [in2.sam|in2.bam|in2.cram] [...]] Computes the depth at each position or region. -i test_SingleEnd_StrandSpecific_hg19.bam -s -o bam2fq_out2 Convert alignments in BAM or SAM format into fastq format.
java -jar picard.jar java -jar picard.jar SamFormatConverter Convert a BAM file to a SAM file, or SAM to BAM. Input and output formats are determined by file extension.
samtools idxstats samtools idxstats in.sam|in.bam|in.cram It retrieves and prints stats in the index file.
java -jar picard.jar java -jar picard.jar ReplaceSamHeader I=input_1.bam HEADER=input_2.bam O=bam_with_new_head.bam Replaces the SAMFileHeader in a SAM or BAM file. This tool makes it possible to replace the header of a SAM or BAM file with the header of anotherfile, or a header block that has been edited manually (in a stub SAM file). The sort order (@SO) of the two input files must be the same.Note that validation is minimal, so it is up to the user to ensure that all the elements referred to in the SAMRecords are present in the new header. -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o output -r hg19.refseq.bed12 For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED format, this program will compare detected splice junctions to reference gene model. splicing annotation is performed in two levels: splice event level and splice junction level.
samtools quickcheck samtools quickcheck [options] in.sam|in.bam|in.cram [ ... ] Quickly check that input files appear to be intact. Checks that beginning of the file contains a valid header (all formats) containing at least one target sequence and then seeks to the end of the file and checks that an end-of-file (EOF) is present and intact (BAM only).
samtools depad samtools depad [-SsCu1] [-T ref.fa] [-o output] <in.bam> Converts a BAM aligned against a padded reference to a BAM aligned against the depadded reference. The padded reference may contain verbatim "*" bases in it, but "*" bases are also counted in the reference numbering. This means that a sequence base-call aligned against a reference "*" is considered to be a cigar match ("M" or "X") operator (if the base-call is "A", "C", "G" or "T"). After depadding the reference "*" bases are deleted and such aligned sequence base-calls become insertions. Similarly transformations apply for deletions and padding cigar operations.
samtools cat samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [ ... ] Concatenate BAMs. The sequence dictionary of each input BAM must be identical, although this command does not check this. This command uses a similar trick to reheader which enables fast BAM concatenation.
samtools bedcov samtools bedcov [INPUT BED] [INPUT BAM1] ... [INPUT BAMn] > [OUTPUT] Calculates read depth for regions listed in a BED dataset using samtools bedcov command
bamtools bamtools random -in input_alignments.bam -out output_alignments_100.bam -n 100 The command bamtools random grabs a random subset of alignments. With the option -n 100, 100 randomly chosen alignments are stored in the output file output_alignments_100.bam.
pints_visualizer pints_visualizer -b sample.bam -o sample -e ExperimentType Extract Transcription Start Sites (TSSs) from a bam file and save extracted signal into strand specific bigwig files
STAR STAR --runMode inputAlignmentsFromBAM --inputBAMfile path/to/bam --option1-name option1-value(s) ... Generate wig files or remove duplicates for a bam file