Differences

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--- mkatari-bioinformatics-august-2013-gatknotes [2014/06/11 13:46] – mkatari
+++ mkatari-bioinformatics-august-2013-gatknotes [2014/06/13 07:23] – 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 121: / Line 121: @@
    -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 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>