Differences

This shows you the differences between two versions of the page.

--- mkatari-bioinformatics-august-2013-gatknotes [2014/06/11 13:46] – mkatari
+++ mkatari-bioinformatics-august-2013-gatknotes [2014/07/02 15:19] – mkatari
@@ Line 38: / Line 38: @@
 bowtie2 -x PTC_Human -U Cohen.fastq -S Cohen.sam
 samtools view -bS Cohen.sam > Cohen.bam
-/code>
+</code>
 The picard method to sort is preferred by GATK
@@ Line 96: / Line 96: @@
 </code>
-Now we merge the bam files and then sort and index them
+In some cases there may be a need to clean the sam/bam file(s) (soft-trimming the coordinates). To do this use CleanSam in Picard tools. You may want to just do it to all to avoid the error in a workflow, but it may not be necessary.
 <code>
-java -jar /export/apps/picard-tools/1.112/MergeSamFiles.jar \
+java -jar /export/apps/picard-tools/1.112/CleanSam.jar \
    INPUT=Sherman.dedup.realign.bam \
+   OUTPUT=Sherman.clean.dedup.realign.bam
+</code>
+Now we merge the bam files and then sort and index them. If you cleaned the bam file, remember to use the cleaned ones.
+<code>
+java -jar /export/apps/picard-tools/1.112/MergeSamFiles.jar \
+   INPUT=Sherman.clean.dedup.realign.bam \
    INPUT=Cohen.dedup.realign.bam \
    OUTPUT=ShermanCohenMerged.bam
@@ Line 110: / Line 118: @@
-Finall !! run gatk
+Finally !! run gatk
 <code>
@@ Line 121: / Line 129: @@
    -glm SNP \
    -o PTC_human.gatk.vcf
+</code>
+If you want to load the vcf file into IGV, remember to index it first.
+<code>
+module load igvtools
+igvtools index PTC_human.gatk.vcf
+</code>
+If you would like to generate a table of from the vcf file use the following command
+<code>
+java -jar /export/apps/GenomeAnalysisTK/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar \
+     -R PTC_Human.fasta
+     -T VariantsToTable \
+     -V PTC_human.gatk.vcf \
+     -F CHROM -F POS -F ID -F QUAL -F AC \
+     -GF GT -GF GQ \
+     -o PTC_human.gatk.vcf.table
 </code>