seandavi

#!/usr/bin/env python
# split a bam file by read group ID
# Sean Davis <[email protected]>
# March 10, 2012
# 
import pysam
import argparse
import logging

logging.basicConfig(level=logging.INFO)

mdshw5

rule screenshot_config:
    input: bam="{dataset}.sort.bam", bai="{dataset}.sort.bam.bai", calls="{dataset}.calls"
    output: batch="{dataset}.igv.batch"
    params: runtime="600", memory="1G", filename="{dataset}.alignments.png"
    run:
        import os.path
        batch_template = """load {bam}
preference SAM.SHOW_CENTER_LINE false
snapshotDirectory {directory}
genome hg38