mkatari-bioinformatics-august-2013-gatknotes
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| mkatari-bioinformatics-august-2013-gatknotes [2014/06/11 13:46] – mkatari | mkatari-bioinformatics-august-2013-gatknotes [2014/06/12 11:59] – mkatari | ||
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| -glm SNP \ | -glm SNP \ | ||
| -o PTC_human.gatk.vcf | -o PTC_human.gatk.vcf | ||
| + | |||
| + | </ | ||
| + | |||
| + | If you want to load the vcf file into IGV, remember to index it first. | ||
| + | |||
| + | If you would like to generate a table of from the vcf file use the following command | ||
| + | < | ||
| + | java -jar GenomeAnalysisTK.jar \ | ||
| + | -R PTC_Human.fasta | ||
| + | -T VariantsToTable \ | ||
| + | -V PTC_human.gatk.vcf \ | ||
| + | -F CHROM -F POS -F ID -F QUAL -F AC \ | ||
| + | -GF GT -GF GQ \ | ||
| + | -o PTC_human.gatk.vcf.table | ||
| </ | </ | ||
mkatari-bioinformatics-august-2013-gatknotes.txt · Last modified: 2016/08/17 08:37 by mkatari