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I have some question with regard on how to move forward to make my analysis more meaningful. As discussed in my previous question with VQSR. I have 10+ RNASeq data sets I have followed the GATK best practices using STAR2pass method. I have now 10+ vcf file using the following commands
gatk -Xmx30048M -T HaplotypeCaller -R Homo_sapiens.GRCh38.dna.primary_assembly.fa -I recal.bam -dontUseSoftClippedBases -stand_call_conf 20.0 -stand_emit_conf 20.0 -o bqsr.vcf
gatk -Xmx30048M -T VariantFiltration -R Homo_sapiens.GRCh38.dna.primary_assembly.fa -V bqsr.vcf -window 35 -cluster 3 -filterName FS -filter "FS'>'30.0" -filterName QD -filter "QD'<'2.0" -o filtered_bqsr.vcf
What I currently do is use bcftools to merge the 10+ vcf file and do the downstream analysis. Should i do joint genotyping instead (my sample size will increase as I move)? I am quite confused which will be the best method.