Changes between Version 41 and Version 42 of SOPs/miningSAMBAM
- Timestamp:
- 03/20/19 15:57:54 (6 years ago)
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SOPs/miningSAMBAM
v41 v42 106 106 107 107 === Remove unmapped reads === 108 109 110 {{{ 111 samtools view -hS -F 4 mapped_unmapped.sam > mapped_only.sam 108 {{{ 109 samtools view -h -F 4 mapped_unmapped.bam | samtools view -bS > mapped_only.bam 110 }}} 111 112 === Extract unmapped reads === 113 {{{ 114 samtools view -h -f 4 mapped_unmapped.bam | samtools view -bS > unmapped_only.bam 112 115 }}} 113 116 … … 116 119 117 120 {{{ 118 samtools view -h S-f 2 mapped_unmapped.sam > mapped.properly_paired.sam121 samtools view -h -f 2 mapped_unmapped.sam > mapped.properly_paired.sam 119 122 }}} 120 123 … … 139 142 140 143 {{{ 141 # Using picard tools, mark duplicates only, this is the default144 # Using Picard tools, mark duplicates only, this is the default 142 145 /pathtojava/java -jar /path_to_picard-tools/picard.jar MarkDuplicates I=input.bam O=ouput.marked_duplicates.bam \ 143 146 M=ouputFileWithStats_metrics.txt REMOVE_DUPLICATES=FALSE 144 147 145 148 146 # Using picard tools, remove duplicates149 # Using Picard tools, remove duplicates 147 150 /pathtojava/java -jar /path_to_picard-tools/picard.jar MarkDuplicates I=input.bam O=ouput.marked_duplicates.bam \ 148 151 M=ouputFileWithStats_metrics.txt REMOVE_DUPLICATES=TRUE
