Question: gatk base recalibration results for 1000 genomes
gravatar for cmo
4.3 years ago by
United States
cmo60 wrote:

I'd bet good money that somebody, probably at Broad Institute, has ran GATK's [BQSR][1] base quality score recalibration) on all of the BAM files for 1000 Genomes (and probably TCGA, etc.) and saved the recalibration table output files somewhere.

Does anybody know if all of the base recalibration tables for 1000 Genomes BAM files are publicly available somewhere?

gatk snp 1000 genomes indel • 1.3k views
ADD COMMENTlink modified 4.2 years ago by Biostar ♦♦ 20 • written 4.3 years ago by cmo60

Hehe, I bet you they saved it somewhere, then deleted it after making the converted BAMs :P Particularly the tables from the second round where you see how much of a difference BQSR made. BQSR by default stores the original quality scores in a tag field though, perhaps it's still there in the final BAM? Probably not though. Alternatively, you could compare the quality scores from the "raw" FASTQ and the BAM to recreate the tables that way. Swap a computational problem for a download bandwidth one.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by John12k
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