HaploMaker

Installation

HaploMaker is cross platform and does not require installation, it only needs java 1.8 or higher environment. Just create a directory and copy MFbio.jar into it.

Files required for pipeline:

1. Fasta reference file and its index (For example arabidopsis.fa and arabidopsis.fa.fai)
2. sorted bam file (For example Chi.bam)
3. VCF file matches bam file (For example chi.vcf)

java -Xmx20g -jar MFbio.jar --task diploidhap --vcf chi.vcf --out haplotypes.hap --afl 400 --seqtype pairedend --minmapq 10 --maxmapq 50 --ref arabidopsis.fa --refx arabidopsis.fa.fai --bam Chi.bam > out.log

Parameter Description

vcf: VCF file
out: output haplotype file
ref: Reference file
refx: Reference file index
bam: sorted BAM file
afl: Average Fragment Length in base pair (In paired-end reads use average of fragments' size in the library, When using single end reads, just use read length here, when using PacBio reads use average length of reads)
seqtype: Use pairedend for illumina paired-end reads, clr for pacbio CLR or subreads and hifi for Pacbio HiFi or CCS reads
minmapq: Minimum read quality MAPQ, reads having quality less than minmapq will be ignored.
maxmapq: Maximum MapQ , it depends on aligner, for Blasr use 50, for BWA, Minimap2 and pbmm2 use 60, for Bowtie2 use 42
Xmx is Java related parameter and controls maximum amount of memory used by Java, adjust it based on memory installed on the machine.