Changes between Version 4 and Version 5 of SOPs/variant_calling_GATK

Timestamp:

01/16/14 15:55:20 (11 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling_GATK

@@ -26 +26 @@
   * bsub "bwa samse /path/to/genome/bwa/genome Reads_1.sai  Reads_1.fq > Reads_1.bwa.sam"
 \\
-'''Convert SAM to BAM, sort, and index''' with [[http://samtools.sourceforge.net/samtools.shtml|samtools]]
+'''Convert SAM to BAM, sort, and index''' with BaRC's streamlined [[http://samtools.sourceforge.net/samtools.shtml|samtools]] commands
   * bsub /nfs/BaRC_Public/BaRC_code/Perl/SAM_to_BAM_sort_index/SAM_to_BAM_sort_index.pl Reads_1.bwa.sam
 \\
-'''Mark duplicates''' (multiple identical reads mapped to the same location). \\
+'''Mark duplicates''' (multiple identical reads mapped to the same location) \\
 Run Picard Tools' [[http://picard.sourceforge.net/command-line-overview.shtml#MarkDuplicates|MarkDuplicates]] on each sample \\
 May Need "VALIDATION_STRINGENCY=LENIENT" if you get  \\