-
Function: Convert alignments in BAM or SAM format into fastq format.
Usage: bam2fq.py -i test_PairedEnd_StrandSpecific_hg19.sam -o bam2fq_out1
-
Function: Copies header from source dataset into target dataset using samtools reheader command.
Usage: samtools reheader [-iP] in.header.sam in.bam
-
Function: According to SAM specification, if Q is the character to represent “base calling quality”
in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that
returns an integer representing the Unicode code point of the character when the argument
is a unicode object, for example, ord(‘a’) returns 97. Phred quality score is widely used
to measure “reliability” of base-calling, for example, phred quality score of 20 means
there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there
is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P,
here P is probability that base-calling is wrong.
Usage: read_quality.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o output
-
Function: Converts BAM dataset to SAM
Usage: samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM]
-
Function: Adds comments to the header of a BAM file.This tool makes a copy of the input bam file, with a modified header that includes the comments specified at the command line (prefixed by @CO). Use double quotes to wrap comments that include whitespace or special characters. Note that this tool cannot be run on SAM files.
Usage: java -jar picard.jar AddCommentsToBam I=input.bam O=modified_bam.bam C=comment_1 C="comment 2"
-
Function: Not to be confused with SortSam which sorts a SAM or BAM file with a valid sequence dictionary, ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped. Runs substantially faster if the input is an indexed BAM file.
Usage: java -jar picard.jar ReorderSam
-
Function: Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file.
Usage: java -jar picard.jar CollectVariantCallingMetrics
-
Function: Generates a BAM index ".bai" file. This tool creates an index file for the input BAM that allows fast look-up of data in a BAM file, lke an index on a database. Note that this tool cannot be run on SAM files, and that the input BAM file must be sorted in coordinate order.
Usage: java -jar picard.jar BuildBamIndex I=input.bam
-
Function: Print header from BAM file(s)
Usage: bamtools header -in input_alignments.bam -out output_alignments_header.txt
-
Function: Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.
Usage: java -jar picard.jar CollectRrbsMetrics R=reference_sequence.fasta I=input.bam M=basename_for_metrics_files
-
Function: The command bamtools revert removes duplicate marks and restores original base qualities.
Usage: bamtools revert -in input_alignments.bam -out output_alignments_reverted.bam
-
Function: Transforms raw Illumina sequencing data into an unmapped SAM or BAM file.
Usage: java -jar picard.jar IlluminaBasecallsToSam BASECALLS_DIR=/BaseCalls/ LANE=001 READ_STRUCTURE=25T8B25T RUN_BARCODE=run15 IGNORE_UNEXPECTED_BARCODES=true LIBRARY_PARAMS=library.params
-
Function: Designs oligonucleotide baits for hybrid selection reactions.
Usage: java -jar picard.jar BaitDesigner TARGET=targets.interval_list DESIGN_NAME=new_baits R=reference_sequence.fasta
-
Function: Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
Usage: java -jar picard.jar CleanSam
-
Function: Collects Illumina lane metrics for the given BaseCalling analysis directory. This tool produces quality control metrics on cluster density for each lane of an Illumina flowcell. This tool takes Illumina TileMetrics data and places them into directories containing lane- and phasing-level metrics. In this context, phasing refers to the fraction of molecules that fall behind or jump ahead (prephasing) during a read cycle.
Usage: java -jar picard.jar CollectIlluminaLaneMetrics RUN_DIR=test_run OUTPUT_DIRECTORY=Lane_output_metrics OUTPUT_PREFIX=experiment1 READ_STRUCTURE=25T8B25T