mkatari-bioinformatics-august-2013-gatknotes
Differences
This shows you the differences between two versions of the page.
| Both sides previous revisionPrevious revision | Next revisionBoth sides next revision | ||
| mkatari-bioinformatics-august-2013-gatknotes [2014/07/02 15:19] – mkatari | mkatari-bioinformatics-august-2013-gatknotes [2014/07/09 07:18] – mkatari | ||
|---|---|---|---|
| Line 40: | Line 40: | ||
| </ | </ | ||
| - | The picard method to sort is preferred by GATK | + | The picard method to sort is preferred by GATK. In some cases PICARD uses the temp directory to do its sorting. You may run into an error that complains about running out of space. To avoid this problem simply create your own tmp directory and tell java that it should use it. See details [[https:// |
| < | < | ||
| - | java -jar / | + | mkdir / |
| + | mkdir / | ||
| + | |||
| + | java -Djava.io.tmpdir=/ | ||
| | | ||
| | | ||
| Line 54: | Line 58: | ||
| < | < | ||
| - | java -jar / | + | java -Djava.io.tmpdir=/ |
| | | ||
| | | ||
| Line 65: | Line 69: | ||
| This will remove any reads that map to the same exact place. It is helpful to get rid of artifacts. | This will remove any reads that map to the same exact place. It is helpful to get rid of artifacts. | ||
| < | < | ||
| - | java -jar / | + | |
| + | java -Djava.io.tmpdir=/ | ||
| | | ||
| | | ||
| | | ||
| | | ||
| - | | + | |
| + | | ||
| </ | </ | ||
| Line 79: | Line 85: | ||
| # | # | ||
| - | java -Xmx2g -jar / | + | java -Xmx2g |
| -T RealignerTargetCreator \ | -T RealignerTargetCreator \ | ||
| -R PTC_Human.fasta \ | -R PTC_Human.fasta \ | ||
| Line 87: | Line 93: | ||
| - | java -Xmx4g -jar / | + | java -Xmx4g |
| -T IndelRealigner \ | -T IndelRealigner \ | ||
| -R PTC_Human.fasta \ | -R PTC_Human.fasta \ | ||
| Line 99: | Line 105: | ||
| < | < | ||
| - | java -jar / | + | java -Djava.io.tmpdir=/ |
| | | ||
| | | ||
| Line 107: | Line 113: | ||
| < | < | ||
| - | java -jar / | + | java -Djava.io.tmpdir=/ |
| | | ||
| | | ||
| Line 121: | Line 127: | ||
| < | < | ||
| - | java -jar / | + | java -Djava.io.tmpdir=/ |
| -T UnifiedGenotyper \ | -T UnifiedGenotyper \ | ||
| -I ShermanCohenMerged.sorted.bam \ | -I ShermanCohenMerged.sorted.bam \ | ||
| Line 140: | Line 146: | ||
| 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 / | + | java --Djava.io.tmpdir=/ |
| -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