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-fastq-file /path/to/file.fastq.gz \
    --out-hap2-fastq-file /path/to/file.fastq.gz \
    --out-hap-unknown-fastq-file /path/to/file.fastq.gz \
    [--missing-from-bam exclude] \
    [--num-threads 4]

Parameters

Parameter	Type	Default	Description
--bam-file	Path	required	Phased BAM file with HP tags.
--fastq-file	Path	required	Original fastq.gz file.
--out-hap1-fastq-file	Path	required	Output fastq.gz for haplotype 1.
--out-hap2-fastq-file	Path	required	Output fastq.gz for haplotype 2.
--out-hap-unknown-fastq-file	Path	required	Output fastq.gz for reads with no HP tag on any alignment, or with conflicting HP tags across alignments.
--missing-from-bam		exclude	How to handle reads in the fastq that are absent from the BAM. ‘exclude’ (default) drops them. ‘unknown’ routes them to –out-hap-unknown. Choices: exclude or unknown.
--num-threads	int	4	Number of htslib threads for BGZF decompression of the phased BAM (default: 4).