Hello,
I have tried using GATK Haplotyper caller. Something, that I noticed is lot of missing genotype calls. Below is the screen shot. Could you suggest if I need to include anything in my parameters that I potentially missed? Also, I Number of SNPS are very low compared to another SNP Calling algortiham which I tested.
echo " java -jar /sc/kzd/home/ponnar02/apps/GATK/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /sc/kzd/proj/bioinfo/dog_snp/Dog_BAM_files/BAM_DUP/merge_bam/SNP_calling/Canis_familiaris_3.1.82_Genome_form.fa -I $i/$i.dedup.good.bam -o $i/$i.realigner.intervals >> RealignerTarget.log"
echo "java -jar /sc/kzd/home/ponnar02/apps/GATK/GenomeAnalysisTK.jar -T IndelRealigner -R /sc/kzd/proj/bioinfo/dog_snp/Dog_BAM_files/BAM_DUP/merge_bam/SNP_calling/Canis_familiaris_3.1.82_Genome_form.fa -I $i/$i.dedup.good.bam -targetIntervals $i/$i.realigner.intervals -o $i/$i.realigned.bam >> $i/IndelRealigner.log"
echo " java -jar /sc/kzd/home/ponnar02/apps/GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R /sc/kzd/proj/bioinfo/dog_snp/Dog_BAM_files/BAM_DUP/merge_bam/SNP_calling/Canis_familiaris_3.1.82_Genome_form.fa -I $i/$i.realigned.bam -ploidy 2 -stand_call_conf 30 -stand_emit_conf 10 -o $i/$i.GATK.raw.vcf"
Have I missed anything. This is a dog genome - A diploid ref .
Thanks,
Rakesh