http://statgen.us/index.php?action=history&feed=atom&title=GATK_IGV_Exercise 2026-04-05T20:09:45Z Revision history for this page on the wiki MediaWiki 1.26.2 http://statgen.us/index.php?title=GATK_IGV_Exercise&diff=263&oldid=prev 2017-02-23T18:49:34Z

<p>Created page with &quot;__NOTITLE__ ==GATK/IGV exercise== java -jar GenomeAnalysisTK.jar --help&lt;br data-attributes=&quot;%20/&quot; /&gt;java -Xmx200m -jar GenomeAnalysisTK.jar -R human_g1k_v37.fa -T UnifiedGeno...&quot;</p> <p><b>New page</b></p><div>__NOTITLE__<br /> ==GATK/IGV exercise==<br /> java -jar GenomeAnalysisTK.jar --help&lt;br data-attributes=&quot;%20/&quot; /&gt;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<br /> less -S ug.vcf&lt;br data-attributes=&quot;%20/&quot; /&gt;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&lt;br data-attributes=&quot;%20/&quot; /&gt;less -S ug.vcf.eval&lt;br data-attributes=&quot;%20/&quot; /&gt;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&lt;br data-attributes=&quot;%20/&quot; /&gt;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</div>

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