Tagged with #bowtie
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Created 2013-06-03 22:42:48 | Updated 2013-06-03 22:44:22 | Tags: gatkpapergenotyper bowtie variant-calling

Comments (6)


I'm trying to call variants from bowtie-aligned reads, I used PrintReads with ReassignMappingQuality filter to give all reads a mapping score of 60 to replace default value of 255. However, I'm wondering if this assignment would introduce any bias in variant calling.

Thanks a lot!