Changes between Version 37 and Version 38 of SOPs/miningSAMBAM

Timestamp:

08/29/17 09:36:34 (7 years ago)

Author:

thiruvil

Comment:

--

SOPs/miningSAMBAM

@@ -36 +36 @@
 }}}
 
+
+
 === Differences between SAM and BAM files ===
 
@@ -48 +50 @@
 === Modify 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:
+In many cases, there's no need to create an intermediate SAM file.
 {{{
-samtools index accepted_hits.bam   # Required if you want to select a genome region (like chrM)
+#to extract selected (mapped to chrM) reads:
+samtools index accepted_hits.bam   # index file 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').
+
 }}}
-We need to keep the header to convert back to BAM (hence the '-h' with 'samtools view' and the '$1 ~ ...' with awk).
+
+{{{
+#extract mulitple regions (eg. chromosomes) into a new bam file
+samtools view -bh -L chromInfo.bed alignment.bam > alignment_chr1_3.bam
+#where chromInfo.bed is a bed file, eg.
+chr1    1       195471971
+chr2    1       182113224
+chr3    1       160039680
+}}}
+
+{{{
+#rename header, eg. use only chr1 to chr3 like above
+samtools reheader newHeader.txt alignment_chr1_3.bam> alignment_chr1_3.newHeader.bam
+#where newheader.txt file is,
+@HD     VN:1.3  SO:coordinate
+@SQ     SN:chr1 LN:195471971
+@SQ     SN:chr2 LN:182113224
+@SQ     SN:chr3 LN:160039680
+@PG     ID:bwa  PN:bwa  VN:0.7.12-r1039 CL:bwa ...
+
+}}}
+
 
 === Count the number of mapped reads ===