mkatari-bioinformatics-august-2013-gatknotes
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mkatari-bioinformatics-august-2013-gatknotes [2016/08/10 20:45] – mkatari | mkatari-bioinformatics-august-2013-gatknotes [2016/08/11 12:28] – mkatari | ||
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module load bowtie2 | module load bowtie2 | ||
module load samtools | module load samtools | ||
+ | module load picard | ||
bowtie2-build PTC_Human.fasta PTC_Human | bowtie2-build PTC_Human.fasta PTC_Human | ||
samtools faidx PTC_Human.fasta | samtools faidx PTC_Human.fasta | ||
- | java -jar / | + | picard CreateSequenceDictionary.jar \ |
| | ||
| | ||
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-o Sample1.dedup.realign.bam | -o Sample1.dedup.realign.bam | ||
+ | |||
+ | GenomeAnalysisTK \ | ||
+ | -T RealignerTargetCreator \ | ||
+ | -R PTC_Human.fasta \ | ||
+ | -I Sample2.dedup.bam \ | ||
+ | -o Sample2forIndelRealigner.intervals | ||
+ | |||
+ | GenomeAnalysisTK \ | ||
+ | -T IndelRealigner \ | ||
+ | -R PTC_Human.fasta \ | ||
+ | -I Sample2.dedup.bam \ | ||
+ | | ||
+ | -o Sample2.dedup.realign.bam | ||
+ | |||
+ | |||
+ | GenomeAnalysisTK \ | ||
+ | -T RealignerTargetCreator \ | ||
+ | -R PTC_Human.fasta \ | ||
+ | -I Sample3.dedup.bam \ | ||
+ | -o Sample3forIndelRealigner.intervals | ||
+ | |||
+ | GenomeAnalysisTK \ | ||
+ | -T IndelRealigner \ | ||
+ | -R PTC_Human.fasta \ | ||
+ | -I Sample3.dedup.bam \ | ||
+ | | ||
+ | -o Sample3.dedup.realign.bam | ||
+ | |||
+ | GenomeAnalysisTK \ | ||
+ | -T RealignerTargetCreator \ | ||
+ | -R PTC_Human.fasta \ | ||
+ | -I Sample4.dedup.bam \ | ||
+ | -o Sample4forIndelRealigner.intervals | ||
+ | |||
+ | |||
+ | GenomeAnalysisTK \ | ||
+ | -T IndelRealigner \ | ||
+ | -R PTC_Human.fasta \ | ||
+ | -I Sample4.dedup.bam \ | ||
+ | | ||
+ | -o Sample4.dedup.realign.bam | ||
</ | </ |
mkatari-bioinformatics-august-2013-gatknotes.txt · Last modified: 2016/08/17 08:37 by mkatari