LUYAO REN
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| FreeBayes uses short-read alignments for any number of individuals from a population and a reference genome to determine the most-likely combination of genotypes for the population at each position in the reference. It reports positions which it finds putatively polymorphic in variant call file format. It can also use an input set of variants (VCF) as a source of prior information, and a copy number variant map (BED) to define non-uniform ploidy variation across the samples under analysis. [1] | FreeBayes uses short-read alignments for any number of individuals from a population and a reference genome to determine the most-likely combination of genotypes for the population at each position in the reference. It reports positions which it finds putatively polymorphic in variant call file format. It can also use an input set of variants (VCF) as a source of prior information, and a copy number variant map (BED) to define non-uniform ploidy variation across the samples under analysis. [1] | ||||
| This pipeline uses BWA-MEM mapper from Sentieon and caller Freebayes. | |||||
| ####**Freebayes default setting:** | ####**Freebayes default setting:** | ||||
| `-C` variants supported by at least 2 observations in a single sample | `-C` variants supported by at least 2 observations in a single sample | ||||
| --genotype-qualities -f ref.fa aln.bam >var.vcf | --genotype-qualities -f ref.fa aln.bam >var.vcf | ||||
| ``` | ``` | ||||
| This pipeline is for Quartet, if you have bam files, please refer to <http://choppy.3steps.cn/renluyao/FreeBayes> | |||||
| ####**Reference** | ####**Reference** | ||||
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