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3. HaplotypeCaller error: Read is malformed: read starts with deletion

Hi, i encountered the same issue (malformed read starts with deletion) and a similar one (malformed read ends with deletion) on two different samples. These are the versions I am using: bwa-0.7.17 ...

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• Kelly Rabionet
• March 18, 2020 09:56
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1. Community
2. Germline
3. how to get rid of haplotypecaller variants caused by weird artificial haplotypes

Hi Bhanu, we have gone through these recommendations several times, we have also increased some of the thresholds to try to remove these variants, but, when considering all samples, even if they re...

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• Kelly Rabionet
• March 16, 2020 16:07
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• 0 votes