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sambamba

Version:
0.6.6
Identifier: TL_bf790f.b6
Tool
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Description


This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats.

Subtools

  • sambamba sort

Links

  • http://www.open-bio.org/wiki/Sambamba

  • http://www.mybiosoftware.com/sambamba-0-5-1-tools-for-working-with-sambam-data.html

  • https://github.com/lomereiter/sambamba

  • https://lomereiter.github.io/sambamba/docs/sambamba-view.html

Tags

DNA
Sequence analysis
RNA-Seq
Sequence analysis

Biostars

  • Pipe from BWA to sambamba
  • How to extract unmapped Paired end reads from BWA output sam file
  • recommended way of filtering out non-karyotype ref sequences and reads from a bam file?
  • sambamba-sort: Error reading BGZF with BAM file
  • MarkDups takes much longer than expected???
  • How to filter both reads of paired end reads by AS when only 1 of the 2 reads has an AS below 50
  • Confused about sambamba syntax for unmapped and mapped
  • sambamba-markdup: unable to move file pointer
  • Sambamba-sort not enough data in stream
  • sambamba markdup command not working
  • Downsample BAM for targeted NGS panels
  • Bamtools stats and samtools flagstat produce different results and confusing my sambamba output.
  • samtools depth and sambamba depth produce different results
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