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Old 12-17-2011, 05:28 PM   #1
Location: Wisconsin

Join Date: Sep 2011
Posts: 10
Default SNP/indel quality


I' am comparing mpileup/bcftools and UnifiedGenotyper.

My data:
7 samples. Reads aligned with tophat against hg19.

Average 'QUAL' in vcf files: UnifiedGenotyper (404), mpileup/bcftools (28).
Average snp/indel calls: UnifiedGenotyper (49,739), mpileup/bcftools (253,933).

Greater than 90% of the tophat-mapped reads had MAPQ of 255. Therefore, when using UnifiedGenotyper, I had to use:"-rf ReassignMappingQuality -DMQ 60".

Can I compare the 'QUAL' field in the vcf output call sets from GATK and SAMtools? My intuition says no. However, I realize GATK uses MAPQ as a cap on base quality. So if anything, the 'QUAL' values for GATK calls are low. I' am still looking into how the SNP/indel calling algorithms use MAPQ.

Any input would be helpful. I' am a novice. Also, I should maybe redo the tophat alignment for correct MAPQ.

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