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I have two strains from small eukariote (say S1 and S2) plus and two reference genomes: G1 (closest to S1 and S2) and sister species G2. Using GATK I can call SNPs in S1 and S2 genomic data. Since G1 and G2 are quite close, I want to get G2 SNPs after performing G2 to G1 alignment. I got MAF file, reduced it (= removed weaker mappings of the same contig to the other part of the genome), then managed to create SAM and sorted BAM file. I used picard to add fake ReadGroups and "MarkDuplicates". In the end I am running:
java -Xmx240G -jar ~/soft/GATK_current/GenomeAnalysisTK.jar -T UnifiedGenotyper -R G1.fa \ -I G1_vs_G2.reduced.gr.dup.bam \ -o G1_vs_G2.reduced.gr.dup.gatk.vcf
I got no running errors, but apart from VCF header the file is empty.
Is there any way to pass some argument to UnifiedGenotyper so it will ignore coverage, and simply call every SNP it encounters?