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Could anyone give me an example generic command for single-sample and multi-sample INDEL calling using the Unified Genotyper? I only found documentation for SNP calling. And when I tried something like that :
java -jar GenomeAnalysisTK.jar \ -R resources/Homo_sapiens_assembly19.fasta \ -T UnifiedGenotyper \ -I input.bam \ --dbsnp dbsnp_137.b37.vcf \ --genotype_likelihoods_model INDEL \ -o output.indels.raw.vcf \ -stand_call_conf 50.0 \ -stand_emit_conf 10.0 \ -dcov 50
The number of indels detected and reported in my output vcf file is too low (only 400 indels for an exome).
Thank you for any help you can provide me, Geoffroy