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
what is Amplicon information ?
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.
To determine the insert size for inferring the original fragments you can try this:
For amplicon aware variant calling you can use:
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.
Ok..Thank you :)
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