Single-Linkage Clustering Of Ngs Reads From A .Bam File

Question

[pmuench]

Hi, is there any existing software to cluster aligned reads form a .bam file with a single-linkage clustering, or a script which generates a distance matrix from a .bam file? thank you!

Answer 1

[Sukhi Singh]

If you know Java or Haskell, there is a question asking what you want here. Check the answers. They are working on sam file which you can convert from bam using samtools samtools view file.bam > file.sam, just in case.

If you want to use some automated tool, use chipster. It includes the clustering options. I met these guys from Finland, the tool looks nice but I haven't tested it yet.

Cheers

[pmuench]

thanks for your answer, but I am not familiar with Haskell. And the Java example dont use single-linkage clustering.