mkatari-bioinformatics-august-2013-gatknotes
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Next revisionBoth sides next revision | |||
mkatari-bioinformatics-august-2013-gatknotes [2014/06/11 12:49] – created mkatari | mkatari-bioinformatics-august-2013-gatknotes [2014/06/11 12:52] – 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 | ||
</ | </ | ||
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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 | ||
</ | </ | ||
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< | < | ||
- | 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 129: | ||
< | < | ||
- | 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