Sam/Bam Manipulation

Function: Computes a number of metrics that are useful for evaluating coverage and performance of sequencing experiments.

Usage: java -jar picard.jar CollectWgsMetricsFromQuerySorted

Function: Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither end of the pair. In addition, this program uses the read-name and extracts the position within the tile whence the read came from. The downsampling is based on this position. Results with the exact same input will produce the same results. Note 1: This is technology and read-name dependent. If your read-names do not have coordinate information, or if your BAM contains reads from multiple technologies (flowcell versions, sequencing machines) this will not work properly. This has been designed with Illumina MiSeq/HiSeq in mind. Note 2: The downsampling is not random. It is deterministically dependent on the position of the read within its tile. Note 3: Downsampling twice with this program is not supported. Note 4: You should call MarkDuplicates after downsampling. Finally, the code has been designed to simulate sequencing less as accurately as possible, not for getting an exact downsample fraction. In particular, since the reads may be distributed non-evenly within the lanes/tiles, the resulting downsampling percentage will not be accurately determined by the input argument FRACTION.

Usage: java -jar picard.jar PositionBasedDownsampleSam

Function: 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.

Usage: samtools calmd [-eubrAESQ] <aln.bam> <ref.fasta>

Supported input format: BAM, CRAM, SAM

Function: Generate index statistics from a BAM fileThis tool calculates statistics from a BAM index (.bai) file, emulating the behavior of the "samtools idxstats" command. The statistics collected include counts of aligned and unaligned reads as well as all records with no start coordinate. The input to the tool is the BAM file name but it must be accompanied by a corresponding index file.

Usage: java -jar picard.jar BamIndexStats I=input.bam O=output

Function: Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments, but only at a set of sampled positions. It is important that the sampled positions be chosen so that they are spread out at least further than a read's length apart; otherwise, you run the risk of double-counting reads in the metrics. If contig-sized intervals are needed, use INTERVALS argument in CollectWgsMetrics.

Usage: java -jar picard.jar CollectWgsMetricsFromSampledSites

Function: This command identifies target regions by examining the continuity of read depth, computes haploid consensus sequences of targets and outputs a SAM with each sequence corresponding to a target. When option -f is in use, BAQ will be applied. This command is only designed for cutting fosmid clones from fosmid pool sequencing [Ref. Kitzman et al. (2010)].

Usage: samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2 em2] [-f ref] <in.bam>

Function: Writes an interval list based on splitting a reference by Ns. This tool identifies positions in a reference where the bases are 'no-calls' and writes out an interval-list using the resulting coordinates. This can be used to create an interval list for whole genome sequence (WGS) for e.g. scatter-gather purposes, as an alternative to using fixed-length intervals. The number of contiguous nocalls that can be tolerated before creating a break is adjustable from the command line.

Usage: java -jar picard.jar ScatterIntervalsByNs R=reference_sequence.fasta OT=BOTH O=output.interval_list

Function: Convert a BAM file to a SAM file, or SAM to BAM. Input and output formats are determined by file extension.

Usage: java -jar picard.jar SamFormatConverter

Function: Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.

Usage: java -jar picard.jar UpdateVcfSequenceDictionary

Function: Convert alignments in BAM or SAM format into fastq format.

Usage: bam2fq.py -i test_SingleEnd_StrandSpecific_hg19.bam -s -o bam2fq_out2

Function: 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.

Usage: junction_annotation.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o output -r hg19.refseq.bed12

Function: It retrieves and prints stats in the index file.

Usage: samtools idxstats in.sam|in.bam|in.cram

Function: 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).

Usage: samtools quickcheck [options] in.sam|in.bam|in.cram [ ... ]

Function: 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.

Usage: java -jar picard.jar ReplaceSamHeader I=input_1.bam HEADER=input_2.bam O=bam_with_new_head.bam

Function: 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.

Usage: samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [ ... ]