Changes between Version 5 and Version 6 of SOPs/miningSAMBAM

Timestamp:

01/31/14 11:17:02 (11 years ago)

Author:

gbell

Comment:

--

SOPs/miningSAMBAM

@@ -35 +35 @@
 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
+samtools index accepted_hits.bam   # Required if you want to select a genome region (like chrM)
+samtools view -h accepted_hits.bam chrM | 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).