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Converting BAM to fastq

SAMtools

# sort paired read alignment .bam file (sort by name -n)
samtools sort -n SAMPLE.bam -o SAMPLE_sorted.bam

# save fastq reads in separate R1 and R2 files
samtools fastq -@ 8 SAMPLE_sorted.bam \
    -1 SAMPLE_R1.fastq.gz \
    -2 SAMPLE_R2.fastq.gz \
    -0 /dev/null -s /dev/null -n


# Using bam2fq
samtools bam2fq SAMPLE.bam > SAMPLE.fastq

paired-end reads:   '/1' or '/2' is added to the end of read names
http://www.htslib.org/doc/samtools.html

How to split a single .fastq file of paired-end reads into two separated files?
# extracting reads ending with '/1' or '/2'
cat SAMPLE.fastq | grep '^@.*/1$' -A 3 --no-group-separator > SAMPLE_r1.fastq
cat SAMPLE.fastq | grep '^@.*/2$' -A 3 --no-group-separator > SAMPLE_r2.fastq

Picard


converting a SAMPLE.bam file into paired end SAMPLE_r1.fastq and SAMPLE_r2.fastq files
java -Xmx2g -jar Picard/SamToFastq.jar I=SAMPLE.bam F=SAMPLE_r1.fastq F2=SAMPLE_r2.fastq
 F2   to get two files for paired-end reads (R1 and R2)
 -Xmx2g   allows a maximum use of 2GB memory for the JVM
http://broadinstitute.github.io/picard/command-line-overview.html#SamToFastq

bam2fastx

http://manpages.ubuntu.com/manpages/quantal/man1/bam2fastx.1.html

Bedtools

bedtools bamtofastq -i input.bam -fq output.fastq

paired-end reads:
samtools sort -n input.bam -o input_sorted.bam   # sort reads by identifier-name (-n)
bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq

http://bedtools.readthedocs.org/en/latest/content/tools/bamtofastq.html