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I'm trying to use GATK to validate reproducibility of the NGS part. We run the same sample 3 times on a MiSeq and I have a list of positions and I want to see if GATK has the same calls in all samples or not.
I'm trying to do it with this command:
RUNX.bam -> input bam files
POSSITIONS.vcf -> vcf with 5035 different positions
java - jar GenomeAnalysisTK -T HaplotypeCaller -R ucsc.hg19.fasta -I RUN1.bam -I RUN2.bam -I RUN3.bam -o RESULT.vcf --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles POSSITIONS.vcf -out_mode EMIT_ALL_SITES
I expected that my result have same amount of positions (calls), but my result only have ~2200