| extract_vscan_counts {poolfstat} | R Documentation |
extract_vscan_counts
Description
Extract VarScan counts
Usage
.extract_vscan_counts(vcf_data, ad_idx, rd_idx)
Arguments
vcf_data |
a matrix of String containing count information in VarScan format |
ad_idx |
the index of the FORMAT AD field |
rd_idx |
the index of the FORMAT RD field |
Details
Extract VarScan counts and return read counts for the reference and alternate allele. For VarScan generated vcf, SNPs with more than one alternate allele are discarded (because only a single count is then reported in the AD fields) making the min.rc unavailable (of vcf2pooldata). The VarScan –min-reads2 option might replace to some extent the min.rc functionality although SNP where the two major alleles in the Pool-Seq data are different from the reference allele (e.g., expected to be more frequent when using a distantly related reference genome for mapping) will be disregarded.
Value
A numeric matrix of read count with nsnp rows and 2*npools columns. The first npools columns consist of read count for the reference allele (RD), columns npools+1 to 2*npools consist of read coverage (RD+AD)
Examples
.extract_vscan_counts(rbind(c("0/0:0:20","1/1:18:1"),c("0/1:12:15","1/1:27:2")),3,2)