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# ReassignMappingQuality and variant calling

Posts: 15
edited June 2013

Hello!

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!

Tagged:

• Posts: 15

Thank you, Carneiro. Bowtie doesn't report mapping qual (255 for not available). Actually I'm just testing if it is okay to use bowtie with gatk.

• Posts: 15

@Geraldine_VdAuwera said:
We do have users who report using data aligned with Bowtie, and assigning qualities using the ReassignMappingQuality filter, but we recommend using an aligner that does report mapping qualities. Having a reasonably accurate estimate of mapping quality empowers the GATK tools to distinguish real variants from artifacts.

Thanks a lot. I got it.

• Posts: 7

bowtie2 reports an 'alignment score' in the optional AS:i and XS:i fields of a SAM file. bowtie2 has some advantages over bwa. instead of pushing bwa maybe gatk ought to consider the AS:i field if it's available.