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  • 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 (http://www.1000genomes.org/wiki/Anal...mat-version-41). 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!

  • #2
    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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    • #3
      Hi guys,

      just use GATK to generate tab from your vfc file.

      MAKING TAB-DELIMITED FILE FROM VCF BY GATK

      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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      • #4
        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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