Difference between revisions of "CallSNPs.py"
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= Stages = | = Stages = | ||
| − | 1. | + | 1. Calculate likelihoods of each possible variant, and apply piror and call variants. |
| − | |||
samtool mpileup -E -d ''NUM'' -DSugB -Q 1 -f ''ref_file'' ''bamfile'' | bcftools view -cgbu - > ''output_bcf_file'' | samtool mpileup -E -d ''NUM'' -DSugB -Q 1 -f ''ref_file'' ''bamfile'' | bcftools view -cgbu - > ''output_bcf_file'' | ||
| + | |||
| + | '''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. | ||
| + | |||
| + | |||
| + | 2. use vcf | ||
Revision as of 17:10, 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. Calculate likelihoods of each possible variant, and apply piror and call variants.
samtool mpileup -E -d NUM -DSugB -Q 1 -f ref_file bamfile | bcftools view -cgbu - > output_bcf_file
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.
2. use vcf
