samtools view -bt ref_list.txt -o aln.bam aln.sam.gz
samtools sort -T /tmp/aln.sorted -o aln.sorted.bam aln.bam
samtools index aln.sorted.bam
samtools idxstats aln.sorted.bam
samtools flagstat aln.sorted.bam
samtools view -bt ref_list.txt -o aln.bam aln.sam.gz
samtools sort -T /tmp/aln.sorted -o aln.sorted.bam aln.bam
samtools index aln.sorted.bam
samtools idxstats aln.sorted.bam
samtools flagstat aln.sorted.bam
# --------------------------------------------------------------------------- | |
# | |
# Description: This file holds all my BASH configurations and aliases | |
# | |
# Sections: | |
# 1. Environment Configuration | |
# 2. Make Terminal Better (remapping defaults and adding functionality) | |
# 3. File and Folder Management | |
# 4. Searching | |
# 5. Process Management |