Generate Chromesome Sizes Reference Files
#!/bin/bash
mm_dir=/home/pipkin/references/GRCm38.102
cd $mm_dir
samtools faidx Mus_musculus.GRCm38.dna_sm.toplevel.fa
cut -f1,2 Mus_musculus.GRCm38.dna_sm.toplevel.fa.fai > GRCm38.genome.sizes
hs_dir=/home/pipkin/references/GRCh38.102
cd $hs_dir
samtools faidx Homo_sapiens.GRCh38.dna_sm.toplevel.fa
cut -f1,2 Homo_sapiens.GRCh38.dna_sm.toplevel.fa.fai > GRCh39.genome.sizes