- samtools
- python
extract_haplotypes.py <bam> <ref_name> <start> <end> <out_prefix> [--bam]
bam bam file
ref_name name of the sequence
start start coordinate
end end coordinate
out_prefix prefix for outfiles
--bam [optional] output reduced bam file
The --bam flag is optional of you want to output the reduced bam for viualisation