extract_nonvscan_counts

.extract_nonvscan_counts

Extract counts from vcf produced by other caller than VarScan (e.g., bcftools, FreeBayes, GATK)

Functions for the computation of f- and D-statistics (estimation of 'Fst', Patterson's 'F2', 'F3', 'F3*', 'F4' and D parameters) in population genomics studies from allele count or Pool-Seq read count data and for the fitting, building and visualization of admixture graphs. The package also includes several utilities to manipulate Pool-Seq data stored in standard format (e.g., such as 'vcf' files or 'rsync' files generated by the the 'PoPoolation' software) and perform conversion to alternative format (as used in the 'BayPass' and 'SelEstim' software). As of version 2.0, the package also includes utilities to manipulate standard allele count data (e.g., stored in 'TreeMix', 'BayPass' or 'SelEstim' format).

Mathieu Gautier

poolfstat

Computing f-Statistics and Building Admixture Graphs Based on
Allele Count or Pool-Seq Read Count Data

extract_nonvscan_counts function

<dl><dt>vcf_data</dt>
<dd>a matrix of String containing count information</dd>
<dt>nb_all</dt>
<dd>a vector containing the number of alleles for the different markers</dd>
<dt>ad_idx</dt>
<dd>the index of the FORMAT AD field</dd>
<dt>min_rc</dt>
<dd>Minimal allowed read count per base (same as min.rc option in <code>vcf2pooldata</code>)</dd></dl>

Arguments

extract_nonvscan_counts — extract_nonvscan_counts

<dl>

<dt>vcf_data</dt>
<dd>a matrix of String containing count information</dd>


<dt>nb_all</dt>
<dd>a vector containing the number of alleles for the different markers</dd>


<dt>ad_idx</dt>
<dd>the index of the FORMAT AD field</dd>


<dt>min_rc</dt>
<dd>Minimal allowed read count per base (same as min.rc option in <code>vcf2pooldata</code>)</dd>

</dl>

extract_nonvscan_counts: extract_nonvscan_counts

Description

Usage

Value

Arguments

Details

Examples