Question

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

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10.9 years ago

Griffan ▴ 90

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 • 3.0k views

ADD COMMENT • link updated 10.9 years ago by Haluk ▴ 190 • written 10.9 years ago by Griffan ▴ 90

score 0 · Answer 1 · 2013-12-25

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10.9 years ago

jackuser1979 ▴ 890

GATK
samtools
VarScan2
SNVmix

ADD COMMENT • link 10.9 years ago by jackuser1979 ▴ 890

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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.

ADD REPLY • link 10.9 years ago by Vivek ★ 2.7k

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That's why I asked.

ADD REPLY • link 10.9 years ago by Griffan ▴ 90

score 0 · Answer 2 · 2013-12-27

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10.9 years ago

Haluk ▴ 190

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

ADD COMMENT • link 10.9 years ago by Haluk ▴ 190