NameThatChrom

Welcome to NameThatChrom Jeopardy!

What is NameThatChrom? This script converts chromosome names in a BAM file from RefSeq to UCSC style, sorts the converted BAM file, and indexes it.

Command-Line Arguments

Argument	Description	Required	Default
input_bam	Input BAM file path.	Yes	N/A
output_bam	Output BAM file path.	Yes	N/A
mapping_file	Space-delimited file mapping RefSeq to UCSC chromosome names (no header).	Yes	N/A
--threads	Number of threads for sorting.	No	8

Note: this does not overwrite the provided BAM file, instead it will make a new one, so be sure to provide a unique name for the new output BAM

How to play

1. Insert your bam file
2. Choos your category: 'RefSeq to UCSC'
3. Get your UCSC-style output and claim your points!

Okay, but really, how to use this tool

1. Locate BAM filed intended for conversion
2. Ensure the 'data/chr_mapping.txt' file contains the desired mappings
3. Run the script

Example Bash Script

If you're working on a Linux based HPC system, here's how you would run the script

#!/bin/bash

#SBATCH -N 1
#SBATCH --mem 200g
#SBATCH -n 1
#SBATCH --cpus-per-task=12
#SBATCH -t 1-00:00:00
#SBATCH --mail-type=end
#SBATCH --mail-user=user@email

# load python
module load python/3.11.9

INPUT_BAM="/path/to/bam/to/convert/sample.bam"
OUTPUT_BAM="path/to/where/new/bam/should/go/sample_converted.bam"
MAPPING_FILE="/data/chr_mapping.txt"


# run script
python /scripts/convert_refseq_to_ucsc_chroms.py \
       --input_bam $INPUT_BAM \
       --output_bam $OUTPUT_BAM \
       --mapping_file $MAPPING_FILE \
       --threads 12