Changes between Version 4 and Version 5 of SOPs/variant_calling

Timestamp:

10/17/13 13:25:04 (12 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling

@@ -38 +38 @@
 }}}
 
-Get uniquely mapping reads
+Get uniquely mapping reads (?)
 {{{
 samtools view -h A_reads.bt2.bam | grep -v XS:i: | samtools view -bS - > A_reads.bt2.sorted_unique.bam
+}}}
+
+Remove duplicated reads assumed to be PCR artifacts (?)
+{{{
+# paired-end reads
+samtools rmdup A_reads.bt2.sorted.bam A_reads.bt2.sorted.noDups.bam
+# single-end reads
+samtools rmdup -s A_reads.bt2.sorted.bam A_reads.bt2.sorted.noDups.bam
 }}}