map_with_bwa_and_remove_PCR_duplicates: Remove PCR duplicates using bwa and Picard
In abshah/RADseqR:

Remove PCR duplicates using bwa and Picard

1 2	map_with_bwa_and_remove_PCR_duplicates(idxbase, in1_fq, in2_fq, threads, output_filename)

`idxbase`	name of bwa index
`in1_fq`	left reads or 1 reads (of pair-end reads) fastq file
`in2_fq`	right or 2 reads (of pair-end reads) fastq file
`threads`	number of threads to run with (depends on server resources)
`output_filename`	output filename (after removing PCR duplicates)