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!
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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