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Do You Guys Have Any Recommendation On Variant Calling Using Long Contigs Or Scaffold

I have assembled a human genome and used bwa mem aligning the contigs back to the reference genome. Do you guys have any recommendation of variant caller?

variant-calling snp sv indel
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updated by Haluk Haluk • written by Griffan • Griffan

2 answers

GATK
samtools
VarScan2
SNVmix

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written by jackuser1979 jackuser1979

I wonder if the regular tools would be appropriate in this scenario since these are not raw reads mapped to reference but assembled contigs and as such the error models would likely be inaccurate.

Not to mention some of the variants here might actually be mis-assembly events.

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written by Vivek Vivek

For the SV/CNV calling, I've used CLEVER and CNVnator.

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written by Haluk Haluk

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