nexus_split_fastq_by_hp_tag

Split a fastq.gz file by HP tag from a phased BAM file.

Usage

nexus_split_fastq_by_hp_tag \
    --bam-file /path/to/file \
    --fastq-file /path/to/file \
    --out-hap1 /path/to/file1.fastq.gz \
    --out-hap2 /path/to/file2.fastq.gz \
    [--missing-from-bam exclude]

Parameters

Parameter	Type	Default	Description
--bam-file		required	Phased BAM file with HP tags.
--fastq-file		required	Original fastq.gz file.
--out-hap1		required	Output fastq.gz for haplotype 1.
--out-hap2		required	Output fastq.gz for haplotype 2.
--missing-from-bam		exclude	How to handle reads in the fastq that are absent from the BAM. ‘exclude’ (default) drops them. ‘both’ writes them to both outputs.