857 bytes added,
18:49, 23 February 2017 __NOTITLE__
==GATK/IGV exercise==
java -jar GenomeAnalysisTK.jar --help<br data-attributes="%20/" />java -Xmx200m -jar GenomeAnalysisTK.jar -R human_g1k_v37.fa -T UnifiedGenotyper -glm BOTH -I child.bam -I father.bam -I mother.bam -L trio.intervals -o ug.vcf
less -S ug.vcf<br data-attributes="%20/" />java -Xmx200m -jar GenomeAnalysisTK.jar -T VariantEval -R human_g1k_v37.fa -L trio.intervals -D dbsnp.vcf -eval ug.vcf -o ug.vcf.eval<br data-attributes="%20/" />less -S ug.vcf.eval<br data-attributes="%20/" />java -Xmx200m -jar GenomeAnalysisTK.jar -R human_g1k_v37.fa -T SelectVariants -V ug.vcf -mv -mvq 0 -o ug.dnm.vcf -ped trio.ped<br data-attributes="%20/" />java -Xmx500m -jar GenomeAnalysisTK.jar -R human_g1k_v37.fa -T HaplotypeCaller -I child.bam -I father.bam -I mother.bam -minPruning 4 -L 1:199325670-199325672 -mergeVariantsViaLD -o hc.vcf