extract_nonvscan_counts {poolfstat}

extract_nonvscan_counts

Description

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

Usage

.extract_nonvscan_counts(vcf_data, nb_all, ad_idx, min_rc)

Arguments

vcf_data

a matrix of String containing count information

nb_all

a vector containing the number of alleles for the different markers

ad_idx

the index of the FORMAT AD field

min_rc

Minimal allowed read count per base (same as min.rc option in vcf2pooldata)

Details

Extract VarScan counts and return read counts for the reference and alternate allele

Value

A numeric matrix of read count with nsnp rows and 2*npools+6 columns. The first npools columns consist of read count for the reference allele, columns npools+1 to 2*npools consist of read coverage. The last 6 columns correspond to the index of the two most frequent alleles (idx_all1 and idx_all2) and their count (cnt_all1 and cnt_all2); the min_rc filtering criterion and count of variant (cnt_bases) other than two first most frequent. The min_rc crit is set to -1 for polymorphisms with more than 2 alleles and with the third most frequent alleles having more than min_rc count

Examples

.extract_nonvscan_counts(rbind(c("0/0:20,0","1/1:1,18"),c("0/2:12,1,15","1/1:27,1,0")),c(2,3),2,0)
.extract_nonvscan_counts(rbind(c("0/0:20,0","1/1:1,18"),c("0/2:12,1,15","1/1:27,1,0")),c(2,3),2,2)