VCF 'QUAL' tool

[lchong]

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!

[Richard Barker]

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

[zgtmann]

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

[aeonsim]

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.