Question: BED file with amplicon information
0
gravatar for a.james
3.7 years ago by
a.james180
Germany
a.james180 wrote:

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

 

 

sequencing rna-seq snp next-gen • 1.6k views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by a.james180
1

what is Amplicon information ?

ADD REPLYlink written 3.7 years ago by Pierre Lindenbaum117k

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. 

ADD REPLYlink written 3.7 years ago by a.james180
1

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:

http://seqanswers.com/forums/showthread.php?t=21512

 

 

ADD REPLYlink written 3.7 years ago by EagleEye6.2k

Ok..Thank you :)

ADD REPLYlink written 3.7 years ago by a.james180
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