marielataretu/samclipy

Filter SAM file for soft-clipped alignments

samclipy

Filter SAM file for soft-clipped alignments

Examples

# Read in.sam and write output to stout
python samclipy.py in.sam

# Read input from stdin and write stdout to file
python samclipy.py < in.sam > out.sam

# Filter alignments from BAM file, write sorted output to file
samtools view -h in.bam | samclipy.py | samtools sort > out.bam

# Filter alignments from BAM file, write all soft-clipped alignments to file
samtools view -h in.bam | samclipy.py --invert | samtools sort > out.bam

Dependencies

• re
• argparse

Full usage

python samclipy.py -h
usage: samclipy [-h] [--minClip MINCLIP] [--invert] [samfile]

Filter SAM file for clipped alignments .

positional arguments:
  samfile

optional arguments:
  -h, --help         show this help message and exit
  --minClip MINCLIP  Required clip length (left + right). If >= 1 total
                     number; if < 1 relative to read length.
  --invert           Output only soft-clipped SAM records and ignore the good
                     ones.

Heavily inspired by

• teloclip
  • splitCIGAR, checkClips, lenCIGAR
• samclip

samclipy's Issues

option for relative number of soft-clipped nts