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 [2014/07/02 15:19] – 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 | ||
- | samtools view -bS Sherman.sam > Sherman.bam | ||
</ | </ | ||
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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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-o Cohen.dedup.realign.bam | -o Cohen.dedup.realign.bam | ||
- | java -Xmx4g -jar /export/ | + | </code> |
- | -T IndelRealigner \ | + | |
- | -R PTC_Human.fasta \ | + | |
- | -I Sherman.dedup.bam \ | + | |
- | -targetIntervals ShermanforIndelRealigner.intervals \ | + | |
- | -o Sherman.dedup.realign.bam | + | |
+ | 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. | ||
+ | |||
+ | < | ||
+ | java -jar / | ||
+ | | ||
+ | | ||
</ | </ | ||
- | Now we merge the bam files and then sort and index them | + | Now we merge the bam files and then sort and index them. If you cleaned the bam file, remember to use the cleaned ones. |
< | < | ||
java -jar / | java -jar / | ||
- | | + | |
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- | Finall | + | Finally |
< | < | ||
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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. | ||
+ | < | ||
+ | module load igvtools | ||
+ | igvtools index PTC_human.gatk.vcf | ||
+ | </ | ||
+ | |||
+ | If you would like to generate a table of from the vcf file use the following command | ||
+ | < | ||
+ | java -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