Copy Number Variants by Derek M. Bickhart

Author:Derek M. Bickhart
Language: eng
Format: epub, pdf
ISBN: 9781493986668
Publisher: Springer New York

4 Notes

1. Pindel has many parameters that you can set to increase speed (multithreading) or change the balance between sensitivity and specificity.

The basic parameters:

-f/--fasta

The reference genome sequences in fasta format

-p/--Pindel-file

The Pindel input file (either this or a bam configuration file is required)

-i/--config-file

The bam config file; either this or a Pindel input file is required. Per line: path and file name of bam, insert size, and sample tag. For example: /data/tumour.bam 400 tumour

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