mkatari-bioinformatics-august-2013-gatknotes
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| Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
| mkatari-bioinformatics-august-2013-gatknotes [2014/06/12 11:59] – mkatari | mkatari-bioinformatics-august-2013-gatknotes [2014/06/13 08:28] – mkatari | ||
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| If you want to load the vcf file into IGV, remember to index it first. | If you want to load the vcf file into IGV, remember to index it first. | ||
| + | < | ||
| + | module load igvtools | ||
| + | igvtools index PTC_human.gatk.vcf | ||
| + | </ | ||
| If you would like to generate a table of from the vcf file use the following command | If you would like to generate a table of from the vcf file use the following command | ||
| < | < | ||
| - | java -jar GenomeAnalysisTK.jar \ | + | java -jar / |
| -R PTC_Human.fasta | -R PTC_Human.fasta | ||
| -T VariantsToTable \ | -T VariantsToTable \ | ||
mkatari-bioinformatics-august-2013-gatknotes.txt · Last modified: 2016/08/17 08:37 by mkatari