mkatari-bioinformatics-august-2013-gatknotes
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mkatari-bioinformatics-august-2013-gatknotes [2014/06/13 07:23] – mkatari | mkatari-bioinformatics-august-2013-gatknotes [2014/07/02 15:19] – mkatari | ||
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- | Now we merge the bam files and then sort and index them | + | In some cases there may be a need to clean the sam/bam file(s) (soft-trimming the coordinates). To do this use CleanSam in Picard tools. You may want to just do it to all to avoid the error in a workflow, but it may not be necessary. |
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- | java -jar / | + | java -jar / |
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+ | Now we merge the bam files and then sort and index them. If you cleaned the bam file, remember to use the cleaned ones. | ||
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+ | java -jar / | ||
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- | Finall | + | Finally |
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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 | ||
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- | 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