mkatari-bioinformatics-august-2013-gatknotes
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mkatari-bioinformatics-august-2013-gatknotes [2014/06/11 13:46] – mkatari | mkatari-bioinformatics-august-2013-gatknotes [2014/07/09 07:18] – 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 | ||
- | /code> | + | </code> |
+ | |||
+ | 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:// | ||
- | The picard method to sort is preferred by GATK | ||
< | < | ||
- | java -jar / | + | mkdir / |
+ | mkdir / | ||
+ | |||
+ | java -Djava.io.tmpdir=/ | ||
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< | < | ||
- | java -jar / | + | java -Djava.io.tmpdir=/ |
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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=/ | ||
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| | ||
| | ||
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- | | + | |
+ | | ||
</ | </ | ||
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# | # | ||
- | java -Xmx2g -jar / | + | java -Xmx2g |
-T RealignerTargetCreator \ | -T RealignerTargetCreator \ | ||
-R PTC_Human.fasta \ | -R PTC_Human.fasta \ | ||
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- | java -Xmx4g -jar / | + | java -Xmx4g |
-T IndelRealigner \ | -T IndelRealigner \ | ||
-R PTC_Human.fasta \ | -R PTC_Human.fasta \ | ||
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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. |
< | < | ||
- | java -jar / | + | java -Djava.io.tmpdir=/ |
| | ||
+ | | ||
+ | </ | ||
+ | |||
+ | 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 -Djava.io.tmpdir=/ | ||
+ | | ||
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- | Finall | + | Finally |
< | < | ||
- | java -jar / | + | java -Djava.io.tmpdir=/ |
-T UnifiedGenotyper \ | -T UnifiedGenotyper \ | ||
-I ShermanCohenMerged.sorted.bam \ | -I ShermanCohenMerged.sorted.bam \ | ||
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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 --Djava.io.tmpdir=/ | ||
+ | -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