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Is there a way to sort BAM files by read name?
Samtools can only create coordinate-sorted BAM indexes in Galaxy. Picard has a queryname sort function and that always outputs a SAM file (even when BAM is input). The Samtools Sort tool will be modified soon. The queryname sort/BAM output should be a failed result and could be considered a bug.
How to visualise BAM files using galaxy IgV?
Visualise BAM files using the Integrative Genomics Viewer (IGV) and identify likely SNVs and indels by eye This workshop uses Galaxy as a platform. It is recommended that participants who have not used Galaxy before either sign up for our Intro to GVL workshop, or work through this tutorial themselves beforehand.
Is there a new sort State for BAMS?
There will be a new datatype for BAMs with a technically “unknown” sort-state in the next release named NativeBAM (can be queryname sorted or left unsorted). Tools that require queryname sorted input will be modified to have the option to re-sort directly on the tool form (some already do, example: Htseq_count).
How to change the name of a galaxy output?
Tip: Galaxy auto-generates a name for all outputs. Therefore, it is advisable to choose a more meaningful name to these outputs. Click on the pencil icon (edit attributes) and change Name e.g. Sample.bam or Sample.sam or Sample.sorted.bam etc.
How are BAM files sorted in samtools index?
Most functionality while using BAM files can be described as such: BAM files are sorted by reference coordinates ( samtools sort) Sorted BAM files are indexed ( samtools index) Take a look here for a detailed manual page for each function in samtools.
When to use tmpprefix.d.bam in SAMtools?
The sorted output is written to standard output by default, or to the specified file ( out.bam ) when -o is used. This command will also create temporary files tmpprefix.%d.bam as needed when the entire alignment data cannot fit into memory (as controlled via the -m option).
Is there a bug in the SAMtools sort tool?
The Samtools Sort tool will be modified soon. The queryname sort/BAM output should be a failed result and could be considered a bug. There will be a new datatype for BAMs with a technically “unknown” sort-state in the next release named NativeBAM (can be queryname sorted or left unsorted).