Convert BAM files to FastQ

Question

[nrk_02]

Hello!

I was wondering about the consequences of converting BAM files to FastQ (maybe with bedtools or samtools). Is there any significant downside of using the FastQ files that are obtained by converting BAMs to FastQ?

Thanks!

Answer 1

[GenoMax]

No downsides but some points to consider below.

After conversion, your fastq data

1. May not contain reads that were not aligned (if unaligned reads were excluded in your BAM). So you can't recreate original full data.
2. May contain some reads multiple times (unless you exclude secondary alignments when you do the conversion)
3. May be hard-clipped in original BAM. So you can't recreate full/original reads.

[atorreso]

May contain some reads multiple times (unless you exclude secondary alignments when you do the conversion)

Is this true when using samtools fastq? I never thought about it!

[swbarnes2]

I think samtools fastq is smart enough to know to ignore reads flagged as secondary and supplemental.