Latest PICARD-tools installation (from v1.124)

PICARD Homepage

http://broadinstitute.github.io/picard/

https://github.com/broadinstitute/picard

Here I am not going to  introduce how excellent and useful this toolset is, but to celebrate the the author finally integrate all tools into one package. So you will not need to find the package name every time you want it. Actually it’s boring to do that: set PICARDHOME or PICARD_HOME to the package root directory and find a package you want, and java –jar PACKAGE_NAME [options] ….

Now I am happy to to see all the functions are integrated into one package ‘picard.jar’. so you would just call

$> java –jar PICARDHOME/picard.jar

Here I am giving my way to install PICARDtools and use it simply.

 

Installation (Linux):

 

1. create a directory you want to install PICARDtools

$> mkdir -p $HOME/programs/picard/v1.124/x86_64

$> cd $HOME/programs/picard/v1.124/x86_64

 

2. Download the software from github

$> wget https://github.com/broadinstitute/picard/releases/download/1.124/picard-tools-1.124.zip

$> unzip picard-tools-1.124.zip

$> ls

picard-tools-1.124

$> mv picard-tools-1.124 bin

$> cd bin

$>ls -1

htsjdk-1.124.jar
libIntelDeflater.so
picard.jar
picard-lib.jar

 

3. [optional] create one link to directly call picard.jar

$> vim picard

#press i on your keyboard to enter VIM edit mode

#pasta following into terminal:

——————————-file border—do not copy this line——————————-

#!/bin/sh

CurDir=$(cd `dirname $(readlink -f $0)`; pwd)

java -jar $CurDir/picard.jar “$@”

——————————file border—–do not copy this line—————————–

#press Esc, and then input :wq to save and exit

#This is to create one file containing content described above. Same with other text editor, like gedit

$> chmod +x ./picard

#And then put this picard file into you PATH by editing ~/.bashrc, /etc/profile or other ways.

$> export PATH=$HOME/programs/picard/v1.124/x86_64/bin:$PATH

in my case, to make the setting immediately work. But remember to change the picardpath to yours.

 

4. test

$> picard

USAGE: PicardCommandLine <program name> [-h]

Available Programs:
————————————————————————————–
Fasta:                                           Tools for manipulating FASTA, or related data.
    CreateSequenceDictionary                     Creates a SAM or BAM file from reference sequence in fasta format
    ExtractSequences                             Extracts intervals from a reference sequence, writing them to a FASTA file
    NormalizeFasta                               Normalizes lines of sequence in a fasta file to be of the same length

————————————————————————————–
Illumina Tools:                                  Tools for manipulating data specific to Illumina sequencers.
    CheckIlluminaDirectory                       Asserts the validity of the data in the specified Illumina basecalling data
    CollectIlluminaBasecallingMetrics            Given an Illumina basecalling and a lane, produces per-lane-barcode basecalling metrics
    CollectIlluminaLaneMetrics                   Collects Illumina lane metrics for the given basecalling analysis directory
    CollectIlluminaSummaryMetrics                Collects summary metrics according to Illumina specifications.
    ExtractIlluminaBarcodes                      Tool to determine the barcode for each read in an Illumina lane
    IlluminaBasecallsToFastq                     Generate fastq file(s) from data in an Illumina basecalls output directory
    IlluminaBasecallsToSam                       Generate a SAM or BAM file from data in an Illumina basecalls output directory
    MarkIlluminaAdapters                         Reads a SAM or BAM file and rewrites it with new adapter-trimming tags

————————————————————————————–
Interval Tools:                                  Tools for manipulating Picard interval lists.
    BedToIntervalList                            Converts a BED file to an Picard Interval List.
    IntervalListTools                            General tool for manipulating interval lists
    LiftOverIntervalList                         Lifts over an interval list from one reference build to another
    ScatterIntervalsByNs                         Writes an interval list based on splitting the reference by Ns

————————————————————————————–
Metrics:                                         Tools for reporting metrics on various data types.
    CalculateHsMetrics                           Calculates Hybrid Selection-specific metrics for a SAM or BAM file
    CollectAlignmentSummaryMetrics               Produces from a SAM or BAM a file containing summary alignment metrics
    CollectBaseDistributionByCycle               Program to chart the nucleotide distribution per cycle in a SAM or BAM file.
    CollectGcBiasMetrics                         Collects information about GC bias in the reads in the provided SAM or BAM
    CollectHiSeqXPfFailMetrics                   Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.
    CollectInsertSizeMetrics                     Writes insert size distribution metrics for a SAM or BAM file
    CollectJumpingLibraryMetrics                 Produces jumping library metrics for the provided SAM/BAMs
    CollectMultipleMetrics                       A “meta-metrics” calculating program that produces multiple metrics for the provided SAM/BAM
    CollectOxoGMetrics                           Collects metrics quantifying the CpCG -> CpCA error rate from the provided SAM/BAM
    CollectQualityYieldMetrics                   Collects a set of metrics that quantify the quality and yield of sequence data from the provided SAM/BAM
    CollectRnaSeqMetrics                         Produces RNA alignment metrics for a SAM or BAM file
    CollectRrbsMetrics                           Collects metrics about bisulfite conversion for RRBS data
    CollectTargetedPcrMetrics                    Produces Targeted PCR-related metrics given the provided SAM/BAM
    CollectWgsMetrics                            Writes whole genome sequencing-related metrics for a SAM or BAM file
    EstimateLibraryComplexity                    Estimates library complexity from the sequence of read pairs
    MeanQualityByCycle                           Writes mean quality by cycle for a SAM or BAM file
    QualityScoreDistribution                     Charts quality score distributions for a SAM or BAM file

————————————————————————————–
Miscellaneous Tools:                             A set of miscellaneous tools.               
    BaitDesigner                                 Designs baits or oligos for hybrid selection reactions.
    FifoBuffer                                   FIFO buffer used to buffer input and output streams with a customizable buffer size

————————————————————————————–
SAM/BAM:                                         Tools for manipulating SAM, BAM, or related data.
    AddCommentsToBam                             Adds comments to the header of a BAM file
    AddOrReplaceReadGroups                       Replaces read groups in a BAM or SAM file with a single new read group
    BamIndexStats                                Generates index statistics from a BAM file
    BamToBfq                                     Create BFQ files from a BAM file for use by the Maq aligner.
    BuildBamIndex                                Generates a BAM index (.bai) file
    CalculateReadGroupChecksum                   Creates a hash code based on the read groups (RG) in the SAM or BAM header.
    CheckTerminatorBlock                         Asserts the provided gzip file’s (e.g., BAM) last block is well-formed; RC 100 otherwise
    CleanSam                                     Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
    CompareSAMs                                  Compares two input SAM or BAM files
    DownsampleSam                                Down-sample a SAM or BAM file to retain a random subset of the reads
    FastqToSam                                   Converts a fastq file to an unaligned BAM or SAM file
    FilterSamReads                               Creates a new SAM or BAM file by including or excluding aligned reads
    FixMateInformation                           Ensure that all mate-pair information is in sync between each read and its mate pair
    GatherBamFiles                               Concatenates one or more BAM files together as efficiently as possible
    MarkDuplicates                               Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.
    MarkDuplicatesWithMateCigar                  Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.
    MergeBamAlignment                            Merges alignment data from a SAM or BAM with data in an unmapped BAM file
    MergeSamFiles                                Merges multiple SAM or BAM files into one file
    ReorderSam                                   Reorders reads in a SAM or BAM file to match ordering in reference
    ReplaceSamHeader                             Replace the SAMFileHeader in a SAM file with the given header
    RevertOriginalBaseQualitiesAndAddMateCigar   Reverts the original base qualities and adds the mate cigar tag to read-group BAMs
    RevertSam                                    Reverts SAM or BAM files to a previous state
    SamFormatConverter                           Convert a BAM file to a SAM file, or a SAM to a BAM
    SamToFastq                                   Converts a SAM/BAM into a FASTQ
    SortSam                                      Sorts a SAM or BAM file
    SplitSamByLibrary                            Splits a SAM or BAM file into individual files by library
    ValidateSamFile                              Validates a SAM or BAM file
    ViewSam                                      Prints a SAM or BAM file to the screen

————————————————————————————–
VCF/BCF:                                         Tools for manipulating VCF, BCF, or related data.
    FilterVcf                                    Hard filters a VCF.
    GatherVcfs                                   Gathers multiple VCF files from a scatter operation into a single VCF file
    GenotypeConcordance                          Calculates the concordance between genotype data for two samples in two different VCFs
    MakeSitesOnlyVcf                             Creates a VCF bereft of genotype information from an input VCF or BCF
    MergeVcfs                                    Merges multiple VCF or BCF files into one VCF file or BCF
    RenameSampleInVcf                            Rename a sample within a VCF or BCF.
    SortVcf                                      Sorts one or more VCF files
    SplitVcfs                                    Splits an input VCF or BCF file into two VCF or BCF files
    UpdateVcfSequenceDictionary                  Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.
    VcfFormatConverter                           Converts a VCF file to a BCF file, or BCF to VCF
    VcfToIntervalList                            Converts a VCF or BCF file to a Picard Interval List.

————————————————————————————–

#To use subfunctions: just call that behind picard, like:

$> picard SamToFastq

#To see options help of SamToFastq

……

 

WORKS. DONE. I am genius…… Ho………HighFive…….

Leave a comment if you think it’s helpful please.