mkatari-bioinformatics-august-2013-gatknotes
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mkatari-bioinformatics-august-2013-gatknotes [2014/06/11 13:36] – mkatari | mkatari-bioinformatics-august-2013-gatknotes [2014/06/11 13:46] – mkatari | ||
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bowtie2 -x PTC_Human -U Cohen.fastq -S Cohen.sam | bowtie2 -x PTC_Human -U Cohen.fastq -S Cohen.sam | ||
samtools view -bS Cohen.sam > Cohen.bam | samtools view -bS Cohen.sam > Cohen.bam | ||
- | bowtie2 -x PTC_Human -U Sherman.fastq -S Sherman.sam | + | /code> |
- | samtools view -bS Sherman.sam > Sherman.bam | + | |
- | </code> | + | |
The picard method to sort is preferred by GATK | The picard method to sort is preferred by GATK | ||
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- | java -jar / | + | |
- | | + | |
- | | + | |
- | | + | |
</ | </ | ||
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< | < | ||
- | java -jar / | ||
- | | ||
- | | ||
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java -jar / | java -jar / | ||
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- | java -jar / | ||
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</ | </ | ||
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< | < | ||
samtools index Cohen.dedup.bam | samtools index Cohen.dedup.bam | ||
- | samtools index Sherman.dedup.bam | ||
# | # | ||
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-o CohenforIndelRealigner.intervals | -o CohenforIndelRealigner.intervals | ||
- | # | ||
- | java -Xmx2g -jar / | ||
- | -T RealignerTargetCreator \ | ||
- | -R PTC_Human.fasta \ | ||
- | -I Sherman.dedup.bam \ | ||
- | -o ShermanforIndelRealigner.intervals | ||
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-targetIntervals CohenforIndelRealigner.intervals \ | -targetIntervals CohenforIndelRealigner.intervals \ | ||
-o Cohen.dedup.realign.bam | -o Cohen.dedup.realign.bam | ||
- | |||
- | java -Xmx4g -jar / | ||
- | -T IndelRealigner \ | ||
- | -R PTC_Human.fasta \ | ||
- | -I Sherman.dedup.bam \ | ||
- | -targetIntervals ShermanforIndelRealigner.intervals \ | ||
- | -o Sherman.dedup.realign.bam | ||
</ | </ |
mkatari-bioinformatics-august-2013-gatknotes.txt · Last modified: 2016/08/17 08:37 by mkatari