adrianodemarino

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

adrianodemarino

Bedtools Cheatsheet

General:

Tools	Description
flank	Create new intervals from the flanks of existing intervals.
slop	Adjust the size of intervals.
shift	Adjust the position of intervals.
subtract	Remove intervals based on overlaps b/w two files.

adrianodemarino

#  ---------------------------------------------------------------------------
#
#  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