unalign bam and convert to fastq

Question

[bioguy24]

I would like to unalign a bam file that was aligned by TMAP and create a fastq file. I am going to re-align using bowtie2 using an indexed hg19 reference. Thank you :).

Answer 1

[thackl]

Have a look at samtools bam2fq

[bioguy24]

Is there a tool or script that can unalign a bam file and output the unaligned bam? Thank you :)

[GouthamAtla]

As said, convert the bam to fastq and re-align with whatever tool you are interested in. Keep in mind about Paired-End, soft/hard clipping etc while converting to fastq.

Or tell what is meant by unaligned bam? Do you mean to say extract unaligned reads from bam?

[bioguy24]

Basically our data has indels in it that are not being called. I have a bam file created using TMAP that I am going to convert to a fastq and realign using bowtie2. Next, I will use bwa on this bam. Does that sound like a goodlan or do you recommend something else? Thank you :).