Bio Alignment Filtering

samtools view -F 4 -o mapped.bam input.bam

samtools view -f 4 -o unmapped.bam input.bam

samtools view -f 2 -o proper.bam input.bam

samtools view -F 1024 -o nodup.bam input.bam

samtools view -F 2304 -o primary.bam input.bam

samtools view -F 256 -F 2048 -o primary.bam input.bam
# Or combined: -F 2304

samtools view -f 64 -o read1.bam input.bam

samtools view -f 128 -o read2.bam input.bam

samtools view -F 16 -o forward.bam input.bam

samtools view -f 16 -o reverse.bam input.bam

samtools view -q 30 -o highqual.bam input.bam

samtools view -F 4 -q 30 -o filtered.bam input.bam

samtools view -o region.bam input.bam chr1:1000000-2000000

samtools view -o regions.bam input.bam chr1:1000-2000 chr2:3000-4000

samtools view -L targets.bed -o targets.bam input.bam

samtools view -q 30 -L targets.bed -o filtered.bam input.bam

# Primary, mapped, non-duplicate, MAPQ >= 30
samtools view -F 3332 -q 30 -o filtered.bam input.bam
# 3332 = 4 (unmapped) + 256 (secondary) + 1024 (duplicate) + 2048 (supplementary)

# Properly paired, primary, no duplicates, MAPQ >= 20
samtools view -f 2 -F 3328 -q 20 -o clean.bam input.bam
# 3328 = 256 (secondary) + 1024 (duplicate) + 2048 (supplementary)
# Note: -f 2 (proper pair) implies mapped, so -F 4 is not strictly needed

# Remove duplicates and low MAPQ
samtools view -F 1024 -q 30 -o filtered.bam input.bam

# Keep ~10% of reads
samtools view -s 0.1 -o subset.bam input.bam

# With seed for reproducibility
samtools view -s 42.1 -o subset.bam input.bam

# Calculate fraction needed
total=$(samtools view -c input.bam)
frac=$(echo "scale=4; 1000000 / $total" | bc)
samtools view -s "$frac" -o subset.bam input.bam

import pysam

with pysam.AlignmentFile('input.bam', 'rb') as infile:
    with pysam.AlignmentFile('filtered.bam', 'wb', header=infile.header) as outfile:
        for read in infile:
            if read.is_unmapped:
                continue
            if read.mapping_quality < 30:
                continue
            if read.is_duplicate:
                continue
            outfile.write(read)

import pysam

def passes_filter(read):
    if read.is_unmapped:
        return False
    if read.is_secondary or read.is_supplementary:
        return False
    if read.is_duplicate:
        return False
    if read.mapping_quality < 30:
        return False
    return True

with pysam.AlignmentFile('input.bam', 'rb') as infile:
    with pysam.AlignmentFile('filtered.bam', 'wb', header=infile.header) as outfile:
        for read in infile:
            if passes_filter(read):
                outfile.write(read)

import pysam

with pysam.AlignmentFile('input.bam', 'rb') as infile:
    with pysam.AlignmentFile('region.bam', 'wb', header=infile.header) as outfile:
        for read in infile.fetch('chr1', 1000000, 2000000):
            outfile.write(read)

import pysam

def read_bed(bed_path):
    regions = []
    with open(bed_path) as f:
        for line in f:
            if line.startswith('#'):
                continue
            parts = line.strip().split('\t')
            regions.append((parts[0], int(parts[1]), int(parts[2])))
    return regions

regions = read_bed('targets.bed')

with pysam.AlignmentFile('input.bam', 'rb') as infile:
    with pysam.AlignmentFile('targets.bam', 'wb', header=infile.header) as outfile:
        for chrom, start, end in regions:
            for read in infile.fetch(chrom, start, end):
                outfile.write(read)

import pysam
import random

random.seed(42)
fraction = 0.1

with pysam.AlignmentFile('input.bam', 'rb') as infile:
    with pysam.AlignmentFile('subset.bam', 'wb', header=infile.header) as outfile:
        for read in infile:
            if random.random() < fraction:
                outfile.write(read)