Difference between revisions of "CallSNPs.py"
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| − | + | The call SNPS.py 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 | + | It requires an alignment in the shape of the base reference sequence and the bam files of the short reads aligned to that sequence (run previously, maybe with '''bwa''' or one of the '''bowtie''' programs). |
= Stages = | = Stages = | ||
Revision as of 15:53, 1 April 2016
The call SNPS.py 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 reads aligned to that sequence (run previously, maybe with bwa or one of the bowtie programs).
Stages
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
