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--- mkatari-bioinformatics-august-2013-gatknotes [2014/07/09 07:18] – mkatari
+++ mkatari-bioinformatics-august-2013-gatknotes [2014/10/09 13:12] – mkatari
@@ Line 153: / Line 153: @@
      -GF GT -GF GQ \
      -o PTC_human.gatk.vcf.table
+</code>
+In order to filter your vcf file based on quality measures, depth, and also statistical significance, you can use variant filter option in the gatk toolkit. Below is an example of suggested filters for data that has low coverage.
+<code>
+java -Xmx2g -jar /export/apps/gatk/3.1.1/GenomeAnalysisTK.jar \
+    -R /home/emasumba/cassavaV5_0.chromsomesRomanNumerals.fa \
+    -T VariantFiltration \
+    -o namikonga_albert_filter.vcf \
+    --variant /home/emasumba/Namikonga_Albert.gatk.vcf \
+    --filterExpression "QD < 2.0 || MQ < 40.0 || FS > 60.0 || HaplotypeScore >13.0" --filterName "mannyfilter"
+</code>
+Finally to save the SNPs that passed your filter, you simply use the selectvariant tool.
+<code>
+java -Xmx2g -jar /export/apps/gatk/3.1.1/GenomeAnalysisTK.jar \
+    -T SelectVariants \
+    --variant namikonga_albert_filter.vcf \
+    -o namikonga_albert_filter_only.vcf \
+    -ef \
+    -R /home/emasumba/cassavaV5_0.chromsomesRomanNumerals.fa
 </code>