mkatari-bioinformatics-august-2013-gatknotes
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| mkatari-bioinformatics-august-2013-gatknotes [2014/06/11 12:52] – mkatari | mkatari-bioinformatics-august-2013-gatknotes [2014/07/02 15:19] – mkatari | ||
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| * create a bam index for dedup bam files | * create a bam index for dedup bam files | ||
| * realign samples | * realign samples | ||
| + | |||
| + | Once they are all processed | ||
| * merge all samples to one bam file | * merge all samples to one bam file | ||
| * sort and index this merged bam file | * sort and index this merged bam file | ||
| Line 36: | Line 38: | ||
| 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 | ||
| </ | </ | ||
| Line 47: | Line 47: | ||
| | | ||
| - | java -jar / | + | |
| - | | + | |
| - | | + | |
| - | | + | |
| </ | </ | ||
| Line 56: | Line 53: | ||
| < | < | ||
| - | java -jar / | ||
| - | | ||
| - | | ||
| - | | ||
| - | | ||
| - | | ||
| - | | ||
| java -jar / | java -jar / | ||
| Line 82: | Line 72: | ||
| | | ||
| - | java -jar / | ||
| - | | ||
| - | | ||
| - | | ||
| - | | ||
| - | | ||
| </ | </ | ||
| Line 93: | Line 77: | ||
| < | < | ||
| samtools index Cohen.dedup.bam | samtools index Cohen.dedup.bam | ||
| - | samtools index Sherman.dedup.bam | ||
| # | # | ||
| Line 102: | Line 85: | ||
| -o CohenforIndelRealigner.intervals | -o CohenforIndelRealigner.intervals | ||
| - | # | ||
| - | java -Xmx2g -jar / | ||
| - | -T RealignerTargetCreator \ | ||
| - | -R PTC_Human.fasta \ | ||
| - | -I Sherman.dedup.bam \ | ||
| - | -o ShermanforIndelRealigner.intervals | ||
| Line 117: | Line 94: | ||
| -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 / | ||
| - | | + | |
| | | ||
| | | ||
| Line 140: | Line 118: | ||
| - | Finall | + | Finally |
| < | < | ||
| Line 151: | Line 129: | ||
| -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