Converting Bam file to Fasta (Zipped)

Question

[Eliveri]

I would like to convert .bam files to fq.gz (zipped fasta files) for paired reads.

bedtools bamtofastq seems to be a commonly recommended method, I have also seen samtools fastq as a possible alternative.

bedtools bamtofastq -i inputfile.bam -fq outputR1.fq -fq2 outputR2.fq 
samtools fastq -@ 8 unmapped_sorted.bam \
  -1 outputR1.fastq.gz \
  -2 outputR2.fastq.gz \
   -0 /dev/null -s /dev/null -n

It seems for bedtools bamtofastq it is not possible to output zipped fasta files.

Is samtools fastq a good alternative?

[iraun]

Hi! Just as an alternative to samtools (which should work), maybe worth trying reformat.sh from BBMap suite as suggested in Converting large (compressed and unsorted) BAM files to fastq

[Eliveri]

Thank you for the suggestion!

[ATpoint]

samtools should be fine: samtools fastq compression

Be sure to use file to manually check that it is indeed gzip-compressed once finished.

[Eliveri]

Thank you for the confirmation and tips!