I would like to ask you, if anyone has experience with filtering out variants, that are not covered in both directions by reads (WES and Gene panels). I am using GATK workflow with haplotype caller and hard filtering, but after all steps it remains even the variants, which are covered only 2+ 0- or 3+ 0- and I want these variants with zero in any direction not to be called.
Any ideas? Thank you very much
Here is syntax of mine HaplotypeCaller command:
java -jar $gatk -T HaplotypeCaller -R hg19.fasta -L bedfile -I sample.bam -o output.g.vcf -nct 16 --emitRefConfidence GVCF --variant_index_type LINEAR --variant_index_parameter 128000 --dontUseSoftClippedBases