Changes between Version 3 and Version 4 of SOPs/miningSAMBAM

Timestamp:

07/18/13 12:16:07 (12 years ago)

Author:

gbell

Comment:

--

SOPs/miningSAMBAM

@@ -25 +25 @@
 Both foo.sorted.bam and foo.sorted.bam.bai are needed for visualization.
  }}}  
+
+=== Process a BAM file into another BAM file ===
+
+In many cases, there's no need to create an intermediate SAM file.  For example, to extract selected (mapped to chrM) reads:
+{{{
+samtools view -h accepted_hits.bam | awk -F "\t" '$3 ~ /chrM/ || $1 ~ /^@/ {print $0}' | samtools view -bS - > ~/accepted_hits.chrM_only.bam
+}}}
+We need to keep the header to convert back to BAM (hence the '-h' with 'samtools view' and the '$1 ~ ...' with awk).
 
 === Count the number of mapped reads ===
@@ -58 +66 @@
 
 
-=== How many multiple/uniquely mapped reads are in a bam/sam file?
+=== How many multiple/uniquely mapped reads are in a bam/sam file? ===
 
 {{{
 bam_stat.py -i mapped_reads.bam >& bam_stat.out.txt
 }}}
+