filter_raw_microhap_data: Filter raw microhaplot output from...

In eriqande/microhaplotopia: Tools for Working with Microhaplot Data a la the SWFSC

Description

Given a set of filtering criteria on individual haplotype depth, total read depth for the genotype and allelle balance (the ratio of read 2 depth to read 1 depth) this function will filter raw amplicon sequencing data. The input file here could be what was loaded into R using the read_unfiltered_observed() function from this package.

Usage

filter_raw_microhap_data(hap_raw, haplotype_depth, total_depth, allele_balance)

Arguments

hap_raw	dataframe of unfiltered haplotypes. This could be from a single run or a large number of runs that have been joined together.
haplotype_depth	remove haplotypes with less than depth specified here. This is for removing what's considered potential genotyping errors or depths you don't feel confident about.
total_depth	minimum number of reads required for the genotype to be retained.
allele_balance	For heterozygotes only. The ratio of the second haplotype read depth to the first haplotype read depth. For example, genotype with read depth of 30 and 20, the allele balance is 0.66

eriqande/microhaplotopia documentation built on July 7, 2020, 1:16 a.m.