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 | 3.1.1.0 | 22.05 | |
revert the original base qualities and add the mate cigar tag | 3.1.1.0 | 22.05 | |
charts the GC bias metrics | 3.1.1.0 | 22.05 | |
Collect metrics to quantify single-base sequencing artifacts | 3.1.1.0 | 22.05 | |
compute metrics for evaluating of whole genome sequencing experiments | 3.1.1.0 | 22.05 | |
perform SAM/BAM grooming | 3.1.1.0 | 22.05 | |
merge alignment data with additional info stored in an unmapped BAM dataset | 3.1.1.0 | 22.05 | |
sort SAM/BAM dataset | 3.1.1.0 | 22.05 | |
assess validity of SAM/BAM dataset | 3.1.1.0 | 22.05 | |
convert Fastq data into unaligned BAM | 3.1.1.0 | 22.05 | |
Downsample a file to retain a subset of the reads | 3.1.1.0 | 22.05 | |
chart distribution of base qualities | 3.1.1.0 | 22.05 | |
include or exclude aligned and unaligned reads and read lists | 3.1.1.0 | 22.05 | |
merges multiple SAM/BAM datasets into one | 3.1.1.0 | 22.05 | |
normalize fasta datasets | 3.1.1.0 | 22.05 | |
examine aligned records in BAM datasets to locate duplicate molecules | 3.1.1.0 | 22.05 | |
compute metrics about datasets generated through hybrid-selection (e.g. exome) | 3.1.1 | 22.05 | |
chart quality score distribution | 3.1.1.0 | 22.05 | |
plots distribution of insert sizes | 3.1.1.0 | 22.05 | |
add or replaces read group information | 3.1.1.0 | 22.05 | |
collect metrics about the alignment of RNA to various functional classes of loci in the genome | 3.1.1.0 | 22.05 | |
add comments to BAM dataset | 3.1.1.0 | 22.05 | |
examine aligned records in BAM datasets to locate duplicate molecules | 3.1.1.0 | 22.05 | |
reorder reads to match ordering in reference sequences | 3.1.1.0 | 22.05 | |
ensure that all mate-pair information is in sync between each read and it's mate pair | 3.1.1.0 | 22.05 | |
assess sequence library complexity from read sequences | 3.1.1.0 | 22.05 | |
convert coordinate data into picard interval list format | 3.1.1.0 | 22.05 | |
extract reads and qualities from SAM/BAM dataset and convert to fastq | 3.1.1.0 | 22.05 | |
charts the nucleotide distribution per cycle in a SAM or BAM dataset | 3.1.1.0 | 22.05 | |
writes a file containing summary alignment metrics | 3.1.1.0 | 22.05 | |
replace header in a SAM/BAM dataset | 3.1.1.0 | 22.05 |