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Samclip container

Main tool: samclip

Basic information on how to use this tool:

  • executable: ./samclip
  • help: -h, --help
  • version: -V, --version
  • description: Filter SAM file for soft and hard clipped alignments

Example Usage

Basic command to clip ends of reads

samclip --ref ref.fa < in.sam > out.sam

Integrate samclip with other tools like bwa and samtools

bwa mem ref.fa R1.fq R2.fq | samclip --ref ref.fa | samtools sort > out.bam