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!