Is it necessary to convert the aligned bam file to unmapped bam file before converting it to fastq files?

Question

[NikhilP]

I was doing mitochondrial analysis using Gatk, in that they first converted bam file to unmapped and then converted it to fastq files for further processing.

So is it necessary to convert the bam to ubam first before converting it to fastq files? If yes, then why? Does it makes any difference if we convert bam to fastq?

Answer 1

[GenoMax]

If you are only interested in getting reads that were unmapped then you should filter the BAM flle (see samtools extract unmapped reads ) before converting the filtered file to fastq data.