for earlier versions of Pindel, multiple bam files for one sample is allowed but recently one bam per sample. if multiple insert sizes are there in one bam file, maximum insert size is recommended. for most paired-end read data, this works fine but if insert size varies from 450 to 2000 as in the example, this strategy is not optimal (decreased sensitivity) for reads with much shorter insert sizes.

please report to kye@genome.wustl.edu if you observe any missing variants or errors during running Pindel. we would like to further improve it.

It can't be done if all the libraries are in the same bam file. But you can split the bam file by library and then mention about each library in config file.

Format (one line for each bam file representing single library):

Location of BAM file Insert size Sample name

For example:

ABC.bam 450 Sample_M

XYZ.bam 900 Sample_M

KLM.bam 2000 Sample_M