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Previously I have been running a command like this:
java -jar /path/GenomeAnalysisTK.jar \ -T UnifiedGenotyper \ -R /path/human_g1k_v37.fasta \ -et NO_ET \ -K /path/key \ -out_mode EMIT_ALL_SITES \ --input_file /path/bam \ -L /path/intervals \ -gt_mode GENOTYPE_GIVEN_ALLELES \ --alleles /path/vcf \ --dbsnp /path/dbsnp_135.b37.vcf \ -o /path/my.vcf
But I was reading the documentation again and I read this statement: GENOTYPE_GIVEN_ALLELES only the alleles passed in from a VCF rod bound to the -alleles argument will be used for genotyping
Which lead me to believe that there wasn't a need to include the lines: --input_file /path/bam \ -L /path/intervals \
because it would be redundant. But when I try to run without those line I get back an error message: Walker requires reads but none were provided.
Can you give an explaination as to why both of those lines AND GENOTYPE_GIVEN_ALLELES would be needed?