converting Indel Realigned Bam to fastq

Question

[IP]

Hi everyone!

My lab is working on an exome-seq pipeline and I have been given the bam files after performing Indel realignment. I want to perform again all the pipeline as sanity check.

I have converted the bam files to fastq using Picard SamtoFastq and when performing the quality control of the fastq files, the plots are not the same, in spite of being similar. Also I am missing 5 millions of reads in respect to the initial fastq files.

Is there way to get the initial fastq files from this Indel Realigned files?

Thanks for reading,

best,

[Pierre Lindenbaum]

Also I am missing 5 millions of reads in respect to the initial fastq files.

did you remove the duplicates ?

[IP]

Hi Pierre! thank you!

Yeah, I guess that they must have remove duplicates, I will write to the company that did the first analysis and see what is going on.

Thanks!

Answer 1

[igor]

As Pierre already mentioned, it's possible that duplicates were removed.

You may have also lost reads that did not align and BAM only has aligned reads. You can check for that with samtools idxstats (if there are no unmapped reads, that is the case).

It's possible that only reads mapped to the target regions were retained in one of the steps.

[IP]

I will check that!

Thanks!