vcftools site quality score -1 in GATK Mutect2 vcf files

Question

[Hasib]

I have run bam files in GATK Mutect2 in "Tumor with matched normal mode" (Tumor+Normal sample) and also in "Tumor only mode" and I have also run them with and without PoN and germline resource file. Whatever I do, running vcftools afterwards for Site Quality check always returns with the value -1 (Negative 1) for each and every single position. What might I be doing wrong? Please help.

[Pierre Lindenbaum]

what is the vcftools command line ?

[Hasib]

vcftools --gzvcf variant call_file.vcf --site-quality --out output_file_name

Answer 1

[Pierre Lindenbaum]

vcftools is deprecated. How about using bcftools ?

--site-quality Generates a file containing the per-site SNP quality, as found in the QUAL column of the VCF file

bcfools query -f '%CHROM\t%POS\t%REF\t%ALT\t%QUAL\n' variant call_file.vcf

of course if variant call_file.vcf doesn't have any value for QUAL, the output will just be '.' for the QUAL column...

[Hasib]

This is what's actually bothering me. Opening up the vcf file, I see the QUAL column has no value ("." only) but running it through vcftools give -1 socre.

[Pierre Lindenbaum]

you don't have any QUAL set in your vcf.

grep -v "^#" variant call_file.vcf | cut -f 6 

[Hasib]

No, I don't. Running the above command returns a long list with only a dot (".") per line. I have trimmed adapter contents from fastq files using trimmomatic, then aligned with reference genome using bwa mem and then ran some additional commands to remove errors from bam files. Then I used GATK Mutect2 to call variants using tumor and matched normal bam files. The resulting vcf files have no QUAL value. I'm new at this and don't know what I'm doing wrong.