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Old 02-23-2012, 08:15 AM   #1
Junior Member
Location: Toronto, Canada

Join Date: Feb 2012
Posts: 2
Default VCF 'QUAL' tool

I'm working on generating some quality statistics for various BAM files. One number I'd like to generate is the confidence of the base call for each base--essentially the QUAL column of the VCF format spec ( However, I don't want to generate an entire VCF file, just a simple tab-delimited file that shows chromosome, position, and genotype confidence score.

I've considered doing the calculation by hand, but I'd like to know if there is some existing tool/function that can accomplish this task for me. Again, I'm not interested in outputting any other data such as the actual base calls--just the confidence scores.

Thanks for your help!
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Old 02-05-2013, 07:36 PM   #2
Richard Barker
Location: Madison wisconsin

Join Date: Apr 2012
Posts: 47

I'm also to trying to generate a VCF (to use to generate counts per gene with some Arabidopsis RNAseq data i have) file for Arabidopsis thaliana but am not sure where to start... any advice
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Old 07-04-2013, 05:55 AM   #3
Location: Czech Republic

Join Date: Feb 2013
Posts: 13

Hi guys,

just use GATK to generate tab from your vfc file.


java -jar GenomeAnalysisTK.jar \
-R reference.fasta
-T VariantsToTable \
-V file.vcf \
-F CHROM -F POS -F ID -F QUAL -F AC \ % what do you want
-o results.table
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Old 07-07-2013, 02:59 PM   #4
Location: Belgium

Join Date: Jun 2011
Posts: 45

Just remember QUAL score will be confounded by Copy Number and SVs present in your individual/population. You'll get some very high QUAL scores for sites in the genome that have higher than expected coverage as lots of reads will appear to support a Variant at that site when actually it should be multiple sites. If you are going to be working with QUAL make sure you apply a Depth of Coverage filter to discard sites with depth of Coverage greater than ~1.2x the average depth of coverage for the sample.
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