variant calling on amplicon data
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7.1 years ago
Richard ▴ 580

Hi all,

Does anyone have a recommended approach for variant calling (SNVs and indels) on human amplicon illumina reads? My bams are aligned with BWA and have had the chastity failed and duplicate reads marked.

If possible, I'd like to be able to apply a variant caller that can be instructed to ignore the duplicate status of the reads, that way we can keep the original bam that is created by our pipeline as well as keep the duplicate reads marked in case that information is needed later.

Thanks!

amplicon variant • 3.8k views
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Amplicons are duplicates by definition. Why mark them in this scenario?

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For now, it is a limitation of our pipeline - that all bams are duplicate marked when they come through.

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Then fix the pipeline?

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Why won't a standard variant calling approach work for your data? If you have BAMs, kick them over to GATK. Reads that fail a duplicate filter (such as the one introduced using the mapping-based approach in Picard) will be handled appropriately, as per GATK's best practices pipeline.

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7.1 years ago
vassialk ▴ 200

Use NextGene software. It has 35 days trial and if you are smart enough, you can use it free for more time than forever.

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If you're going to recommend a commercial solution, I don't think advocating pirating it is really necessary when there are a plethora of open source tools that will do exactly what the OP wants. If you're using NextGene then you clearly appreciate what the software developers have done. So stump up the cash in appreciation, or learn to use an open source toolchain.

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7.1 years ago
Zaag ▴ 800

I just align them with BWA, sort with samtools and call variants with GATKs Haplotypecaller.

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