| SAM (Sequence Alignment/Map) is a generic format for storing large nucleotide sequence alignments. Picard comprises Java-based utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported. |
hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/picard
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| revert SAM/BAM datasets to a previous state | 2.18.2.1 | 16.01 | |
| revert the original base qualities and add the mate cigar tag | 2.18.2.1 | 16.01 | |
| charts the GC bias metrics | 2.18.2.1 | 16.01 | |
| Collect metrics to quantify single-base sequencing artifacts | 2.18.2.1 | 16.01 | |
| compute metrics for evaluating of whole genome sequencing experiments | 2.18.2.1 | 16.01 | |
| perform SAM/BAM grooming | 2.18.2.1 | 16.01 | |
| merge alignment data with additional info stored in an unmapped BAM dataset | 2.18.2.1 | 16.01 | |
| sort SAM/BAM dataset | 2.18.2.1 | 16.01 | |
| assess validity of SAM/BAM dataset | 2.18.2.1 | 16.01 | |
| convert Fastq data into unaligned BAM | 2.18.2.2 | 20.01 | |
| Downsample a file to retain a subset of the reads | 2.18.2.1 | 16.01 | |
| chart distribution of base qualities | 2.18.2.1 | 16.01 | |
| include or exclude aligned and unaligned reads and read lists | 2.18.2.1 | 16.01 | |
| merges multiple SAM/BAM datasets into one | 2.18.2.1 | 16.01 | |
| normalize fasta datasets | 2.18.2.1 | 16.01 | |
| examine aligned records in BAM datasets to locate duplicate molecules | 2.18.2.2 | 16.01 | |
| compute metrics about datasets generated through hybrid-selection (e.g. exome) | 2.18.2 | 16.01 | |
| chart quality score distribution | 2.18.2.1 | 16.01 | |
| plots distribution of insert sizes | 2.18.2.1 | 16.01 | |
| add or replaces read group information | 2.18.2.1 | 16.01 | |
| collect metrics about the alignment of RNA to various functional classes of loci in the genome | 2.18.2.2 | 16.01 | |
| add comments to BAM dataset | 2.18.2.1 | 16.01 | |
| examine aligned records in BAM datasets to locate duplicate molecules | 2.18.2.3 | 16.01 | |
| reorder reads to match ordering in reference sequences | 2.18.2.1 | 16.01 | |
| ensure that all mate-pair information is in sync between each read and it's mate pair | 2.18.2.1 | 16.01 | |
| assess sequence library complexity from read sequences | 2.18.2.1 | 16.01 | |
| convert coordinate data into picard interval list format | 2.18.2.1 | 16.01 | |
| extract reads and qualities from SAM/BAM dataset and convert to fastq | 2.18.2.2 | 16.01 | |
| charts the nucleotide distribution per cycle in a SAM or BAM dataset | 2.18.2.1 | 16.01 | |
| writes a file containing summary alignment metrics | 2.18.2.1 | 16.01 | |
| replace header in a SAM/BAM dataset | 2.18.2.1 | 16.01 | |