From wiki
Revision as of 16:48, 1 April 2016 by Rf (talk | contribs)
Jump to: navigation, search

This script is part of "script_tools" modules.

It requires an alignment in the shape of the base reference sequence and the bam files of the short read aligned to that sequence (run previously, maybe with bwa or one of the bowtie programs).


1. samtools mpileup and bcftools view -cg mpileup collects summary information from the input BAMs and then computes and stores the likelihood of data given each possible genotype. bcftools applies to prior and then calls the variants. To show the options used, the command looks as follows:

samtool mpileup -E -d 'NUM' -DSugB -Q 1 -f 'ref_file' 'bamfile' | bcftools view -cgbu - > 'output_bcf_file'