add VAF to VCF

Question

[Roy]

Hello all,

I use GATK to go from BAM to VCF, however I do not feel as if I receive characteristics like other VCFs I see. The GATK pipeline recommends this code below, and I am wondering if there is a better way to do this?

gatk VariantFiltration \
-R $refpath \
-V raw_snps.vcf \
--filter-name "FAIL_QD" \
--filter-expression "QD < 2.0" \
--filter-name "FAIL_FS" \
--filter-expression "FS > 60.0" \
--filter-name "FAIL_MQ" \
--filter-expression "MQ < 40.0" \
--filter-name "FAIL_SOR" \
--filter-expression "SOR > 10.0" \
-O filtered_snps.vcf

To assist, below with hashtags is my info section with the output of most being AC=2;AF=1.00;AN=2;DP=2. The read depth averages 2 which seems weird. Here is how I added the read groups:

bwa mem -M -t 8 -R '@RG\tID:Lane1\tPU:2\tSM:Sample\tPL:Illumina\tLB:1' $refpath $TRIM1 $TRIM2 > output.sam

INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">

INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">

INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">

INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">

INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">

Any help is appreciated!

[brunobsouzaa]

That command is going to give you values like PASS or not into the FILTER field of your VCF file.

If you want to have VAF, you can use bcftools for that. You can try something like (not tested):

bcftools +fill-tags ${i}.vcf.gz -Oz -o ${i}_MAF.vcf.gz -- -t VAF