samtools_indexing_hap1.pbs

#!/bin/bash
#PBS -q condo05
#PBS -l select=1:ncpus=32:mem=250GB
#PBS -l walltime=168:00:00
#PBS -W group_list=x-ccast-prj-hulke
#PBS -N samtoolsFun

cd /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/HifiParentalIlluminaOmniCAssembly/pre_alignment_processing

#1. indexing of the fasta haplotype contigs file 

module load samtools

#samtools faidx /mmfs1/projects/brent.hulke/MutagenesisSmart/HudsonAlpha/HifiParentalIlluminaOmniCAssembly/gfastats_trio/Sunflower_1_Hetero_Red_trioBinning.asm.dip.hap1.p_ctg.fasta


#indexed file is saved in the folder where the fasta file is located

#2. printing the first two columns into a new file and generating the genome file 

cut -f1,2 Sunflower_1_Hetero_Red_trioBinning.asm.dip.hap1.p_ctg.fasta.fai > triobinning_hap1.genome