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Old 07-10-2012, 06:36 AM   #1
Genomics101
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Default Why is bcftools missing back-to-back/high-divergence-region SNPs (BWA mapping)?

Greetings.

I am doing some SNP-/variant-calling, mapping to a somewhat divergent reference genome (probably about 1.5-2% different), but synteny is preserved.

I have been fine-tuning my SNP-calling using SAMtools/bcftools, however I am still getting false negatives in regions of high divergence (~10-20% difference) and (often, but not always) when two SNPs are next to each other. It looks like the caller is probably inserting gaps in these regions rather than calling them as SNPs, but there are no indels in corresponding regions in the VCF.

Even looking at the unfiltered variant calls, nothing shows up in these regions, and they are the interesting ones.

All help is appreciated. Thanks!
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Old 07-23-2012, 01:08 PM   #2
Genomics101
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Default

If anyone checks, I answered by own question, it was the BAQ correction. Using the extended BAQ brought back the false negatives.
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