BED file with amplicon information

Question

[a.james]

Hello All,

I am looking for a method to convert BAM format into BED format with Amplicon information in it. I mean I need a column which has Amplicon information in it in my BED file

Thanks for any suggestions

[Pierre Lindenbaum]

what is Amplicon information ?

[a.james]

The BED file contains a single track of the genomic regions of the expected PCR amplicons for all probes in the design. It also lists the Amplicon ID and strand for each amplicon.

[EagleEye]

To determine the insert size for inferring the original fragments you can try this:

https://www.cgat.org/downloads/public/cgat/documentation/scripts/bam2bed.html

For amplicon aware variant calling you can use:

https://github.com/AstraZeneca-NGS/VarDict

Or, If you still want to extract the Amplicon location. I am afraid there is no direct solution for that because it is bit complex task. But is is not impossible...you can read this discussion.

[a.james]

Ok..Thank you :)