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I was using GATK UnifiedGenotyper for SNPs/indels. My command is as follows:
java -Xmx16g -jar $gatkPath/GenomeAnalysisTK.jar \ -T UnifiedGenotyper \ -R $humanRefSequence \ -I "$sampleID".recal.bam \ --dbsnp $humanDbsnpFile \ -stand_call_conf 30.0 \ -stand_emit_conf 10.0 \ -dcov 250 \ -l INFO -log "$sampleID".GATKvariants.log \ -o "$sampleID".GATKvariants.raw.vcf \ --output_mode EMIT_ALL_SITES
When I am selecting Indels from the vcf file, it's producing an empty vcf file (which is working fine with SNPs). My command for selecting Indels are as follows:
java -Xmx10g -jar $gatkPath/GenomeAnalysisTK.jar \ -T SelectVariants \ -R $humanRefSequence \ --variant "$sampleID".GATKvariants.raw.vcf \ -o "$sampleID".GATKindels.raw.vcf \ -selectType INDEL \ -log "$sampleID".SelectIndels.log
Do I need to use "-glm BOTH" in UnifiedGenotyper to output both SNPs and Indels? As from the documentation, I understand that the default value of -glm is set to SNP.
Many thanks in advance.