mkatari-bioinformatics-august-2013-gatknotes
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| Next revision | Previous revisionNext revisionBoth sides next revision | ||
| mkatari-bioinformatics-august-2013-gatknotes [2014/06/11 12:49] – created mkatari | mkatari-bioinformatics-august-2013-gatknotes [2014/06/11 13:36] – mkatari | ||
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| 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 / | + | java -jar / |
| + | R=PTC_Human.fasta | ||
| + | O=PTC_Human.dict | ||
| </ | </ | ||
| Line 27: | Line 29: | ||
| * 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 40: | Line 44: | ||
| The picard method to sort is preferred by GATK | The picard method to sort is preferred by GATK | ||
| < | < | ||
| - | java -jar / | + | java -jar / |
| - | java -jar / | + | INPUT=Cohen.bam |
| + | OUTPUT=Cohen.sorted.bam | ||
| + | SORT_ORDER=coordinate | ||
| + | |||
| + | java -jar / | ||
| + | INPUT=Sherman.bam | ||
| + | OUTPUT=Sherman.sorted.bam | ||
| + | SORT_ORDER=coordinate | ||
| </ | </ | ||
| Line 47: | Line 58: | ||
| < | < | ||
| - | java -jar / | + | java -jar / |
| + | INPUT=Sherman.sorted.bam | ||
| + | OUTPUT=ShermanRG.bam | ||
| + | RGLB=Sherman | ||
| + | RGPL=IonTorrent | ||
| + | RGPU=None | ||
| + | RGSM=Sherman | ||
| - | java -jar / | + | java -jar / |
| + | INPUT=Cohen.sorted.bam | ||
| + | OUTPUT=CohenRG.bam | ||
| + | RGLB=Cohen | ||
| + | RGPL=IonTorrent | ||
| + | RGPU=None | ||
| + | RGSM=Cohen | ||
| </ | </ | ||
| 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 -jar / |
| + | INPUT=CohenRG.bam | ||
| + | OUTPUT=Cohen.dedup.bam | ||
| + | METRICS_FILE=Cohen.dedup.metrics | ||
| + | REMOVE_DUPLICATES=TRUE | ||
| + | ASSUME_SORTED=TRUE | ||
| - | java -jar / | + | java -jar / |
| + | INPUT=ShermanRG.bam | ||
| + | OUTPUT=Sherman.dedup.bam | ||
| + | METRICS_FILE=Sherman.dedup.metrics | ||
| + | REMOVE_DUPLICATES=TRUE | ||
| + | ASSUME_SORTED=TRUE | ||
| </ | </ | ||
| Line 98: | Line 131: | ||
| < | < | ||
| - | java -jar / | + | java -jar / |
| + | INPUT=Sherman.dedup.realign.bam | ||
| + | INPUT=Cohen.dedup.realign.bam | ||
| + | OUTPUT=ShermanCohenMerged.bam | ||
| samtools sort ShermanCohenMerged.bam ShermanCohenMerged.sorted | samtools sort ShermanCohenMerged.bam ShermanCohenMerged.sorted | ||
| + | |||
| samtools index ShermanCohenMerged.sorted.bam | samtools index ShermanCohenMerged.sorted.bam | ||
| </ | </ | ||
mkatari-bioinformatics-august-2013-gatknotes.txt · Last modified: 2016/08/17 08:37 by mkatari