Pindel And Multiple Insert Size Libraries Per Bam File
Entering edit mode
8.7 years ago

When running Pindel, the expected insert size is specified for each bam file in the config file.

What should be done when there are 3 libraries with 3 different insert sizes in one bam file.

Is there a way to indicate there is 3 libraries and their insert-sizes? Are varying insert size libraries in a bam file handled with pindel?

pindel • 3.2k views
Entering edit mode
8.6 years ago
liangkaiye ▴ 250

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 if you observe any missing variants or errors during running Pindel. we would like to further improve it.

Entering edit mode
8.7 years ago

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


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