Hello GATK,
I'm using GATK 4.0.6 HaplotypeCaller to call wild bird SNP and InDel sites.
Command
nohup java -jar /opt/GATK-4.0.6/GATK-4.0.6-local.jar HaplotypeCaller -R bird_genome_reference.fa -I input.bam --minimum-mapping-quality 25 -mbq 13 -O VCF_two_type/HC.vcf --output-mode EMIT_VARIANTS_ONLY &
When I check the output in nohup, I notice that there are many optional arguments in the nohup file.
But I didn't see some of them in the ToolDoc of HaplotypeCaller.
Why do not put all the available arguments in the ToolDoc?
I want to set the threshold condition of two short variants caller(bcftools mpileup & HaplotypeCaller) the same as possible and then get the consistent short variants site with SelectVariants to improve my SNP & Indels quality.