CollectSequencingArtifactMetrics

How to install

• This tools requires samtools and zlib to compile. Please follow the link and install samtools first.

• Successful installation of samtools results in the following files (presumably in /usr/local):

  /usr/local/include/zlib.h
  /usr/local/include/bam.h
  /usr/local/include/htslib/*.h
  /usr/local/lib/libz.a
  /usr/local/lib/libbam.a
  /usr/local/lib/libhts.a
  

• Compile csam

  run make or

  gcc -o csam csam.c -lhts -lbam -lz
  

  or

  gcc -I/usr/local/include -L/usr/local/lib -o csam csam.c -lhts -lbam -lz
  

  incase gcc can't find the headers or libs

How to use it

csam -i <bam> -r <ref> -p <prefix>

Output files

${prefix}.pre_adapter_detail_metrics.txt
${prefix}.bait_bias_detail_metrics.txt

Caveats

CONTEXT_SIZEs other than 1 are not yet supported in this implementation.

Reference

Picard CollectSequencingArtifactMetrics