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ReassignMappingQuality and variant calling

gatk2013gatk2013 Posts: 15Member
edited June 2013 in Ask the GATK team


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!

Post edited by gatk2013 on

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