BED file with amplicon information
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7.5 years ago
a.james ▴ 240

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

RNA-Seq SNP next-gen-sequencing • 3.1k views
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what is Amplicon information ?

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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.

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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.

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Ok..Thank you :)

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