reads used for variant calling

Hello!

I have pair-end sequencing data. If read1 is mapping uniquely, read 2 is mapped to multiple locations equally. And read1 and read2 are proper mapped (within the fragment size range, and the strands are also OK (head to head)). Will these reads be used in variant calling (HaplotypeCaller and UnifiedGenotyper)?

thanks,

Ying

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by Sheila

Issue Number
187
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closed
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vdauwera

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