Changes between Version 44 and Version 45 of SOPs/miningSAMBAM

Timestamp:

09/21/20 16:03:12 (5 years ago)

Author:

gbell

Comment:

--

SOPs/miningSAMBAM

@@ -6 +6 @@
 
 All fields in a SAM/BAM file are explained in the [http://samtools.github.io/hts-specs/SAMv1.pdf Sequence Alignment/Map Format Specification].
-
-=== Convert, sort, and/or index ===
-
-{{{
-# Convert SAM to BAM:
-samtools view -bS -o foo.bam foo.sam
-}}}
-
-{{{
-# Convert BAM to SAM:
-samtools view -h -o foo.sam foo.bam
-}}}
-{{{
-# Sort BAM file (where ".bam" is added to "foo.sorted")
-samtools sort foo.bam -T foo > foo.sorted.bam
-}}}
-{{{
-# Index a sorted BAM file (which creates foo.sorted.bam.bai):
-samtools index foo.sorted.bam
-    
-# Both foo.sorted.bam and foo.sorted.bam.bai are needed for visualization.
- }}}
-
-All three steps (SAM=>BAM, sorting, and indexing) can be merged into one command.  See
-{{{
-/nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl
-# Or on a folder of SAM files
-for samFile in `/bin/ls *.sam`; do bsub /nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl $samFile ; done
-}}}
-
 
 
@@ -48 +18 @@
   * For archiving purposes, keep only the BAM file.  The SAM file can easily be regenerated (if ever needed).
 
+=== Convert, sort, and/or index ===
+
+{{{
+# Convert SAM to BAM:
+samtools view -bS -o foo.bam foo.sam
+}}}
+
+{{{
+# Convert BAM to SAM:
+samtools view -h -o foo.sam foo.bam
+}}}
+{{{
+# Sort BAM file (where ".bam" is added to "foo.sorted")
+samtools sort foo.bam -T foo > foo.sorted.bam
+}}}
+{{{
+# Index a sorted BAM file (which creates foo.sorted.bam.bai):
+samtools index foo.sorted.bam
+    
+# Both foo.sorted.bam and foo.sorted.bam.bai are needed for visualization.
+ }}}
+
+All three steps (SAM=>BAM, sorting, and indexing) can be merged into one command.  See
+{{{
+/nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl
+# Or on a folder of SAM files
+for samFile in `/bin/ls *.sam`; do bsub /nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl $samFile ; done
+}}}
+
 === Modify a BAM file into another BAM file ===
 
@@ -60 +59 @@
 
 {{{
-#extract mulitple regions (eg. chromosomes) into a new bam file
+#extract multiple regions (e.g., 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.
+#where chromInfo.bed is a bed file, e.g.,
 chr1    1       195471971
 chr2    1       182113224
@@ -69 +68 @@
 
 {{{
-#rename header, eg. use only chr1 to chr3 like above
+#rename header, e.g., 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,