Changes between Version 19 and Version 20 of SOPs/variant_calling_GATK

Timestamp:

08/11/16 12:00:42 (8 years ago)

Author:

gbell

Comment:

--

SOPs/variant_calling_GATK

@@ -28 +28 @@
 \\ 
 2 - '''Create a genome dictionary.''' [Need to do just once, with Picard's [[http://picard.sourceforge.net/command-line-overview.shtml#CreateSequenceDictionary|CreateSequenceDictionary]].]
-  * java -jar /usr/local/share/picard-tools/CreateSequenceDictionary.jar R=/path/to/genome/genome.fa O=/path/to/genome/genome.dict 
+  * java -jar /usr/local/share/picard-tools/picard.jar CreateSequenceDictionary R=/path/to/genome/genome.fa O=/path/to/genome/genome.dict 
 \\
 3 - '''Validate VCF file or known variants''' (with GATK's [[http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_ValidateVariants.html|ValidateVariants]])
@@ -47 +47 @@
 May Need "VALIDATION_STRINGENCY=LENIENT" if you get  \\
 Exception in thread "main" net.sf.samtools.SAMFormatException: SAM validation error: ERROR: ... MAPQ should be 0 for unmapped read. \\
-  * bsub java -jar /usr/local/share/picard-tools/MarkDuplicates.jar I=Reads_1.bwa.sorted.bam O=Reads_1.bwa.dedup.bam M=Reads_1.bwa.dedup.txt VALIDATION_STRINGENCY=LENIENT
+  * bsub java -jar /usr/local/share/picard-tools/picard.jar MarkDuplicates I=Reads_1.bwa.sorted.bam O=Reads_1.bwa.dedup.bam M=Reads_1.bwa.dedup.txt VALIDATION_STRINGENCY=LENIENT
 \\
 7 - '''Add Read Group header information to each BAM file''' (or GATK won't let you continue) \\
 Run Picard Tools' [[http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadGroups|AddOrReplaceReadGroups]] on each sample. \\
 Specify RGSM (Read Group sample), RGLB (Read Group Library), RGPL (Read Group platform), and RGPU (Read Group platform unit [e.g. run barcode])
-  * bsub java -jar /usr/local/share/picard-tools/AddOrReplaceReadGroups.jar I=Reads_1.bwa.dedup.bam O=Reads_1.bwa.dedup.good.bam RGSM=My_sample RGLB=My_project RGPL=illumina RGPU=none VALIDATION_STRINGENCY=LENIENT
+  * bsub java -jar /usr/local/share/picard-tools/picard.jar AddOrReplaceReadGroups I=Reads_1.bwa.dedup.bam O=Reads_1.bwa.dedup.good.bam RGSM=My_sample RGLB=My_project RGPL=illumina RGPU=none VALIDATION_STRINGENCY=LENIENT
 \\
 8 - '''Index BAM file(s)''' with [[http://samtools.sourceforge.net/samtools.shtml|samtools]] (optional; for IGV viewing)