GATK UnifiedGenotyper SNP calling with Agilent 50Mb target enrichment

nullalleles · 07-12-2011, 12:22 PM

I am trying (and failing) to call SNPs using a reference file (.BED) specifically for the Agilent 50Mb Sureselect enrichment sequencing. I am using the GATK UnifiedGenotyper with the following commands. Any ideas? Thanks!

java -jar ~/Sting/dist/GenomeAnalysisTK.jar \
-R ~/Documents/refFASTA/SureSelect_All_Exon_50mb.bed \
-l INFO \
-T UnifiedGenotyper \
-I ~/Documents/next_gen/sorted.N.dupesremoved.recali.bam \
-o ~/Documents/SNP/N_AgilentSS_50MB_gatk.vcf \
-stand_call_conf 50.0 \
-stand_emit_conf 10.0 \
-dcov 150

nullalleles · 07-18-2011, 07:28 AM

The above code should have contained the argument "-L" for the interval list (bed) file and also a "-R" for the reference fasta file!

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07-12-2011, 12:22 PM	#1
nullalleles Junior Member Location: Michigan Join Date: Jun 2011 Posts: 5	GATK UnifiedGenotyper SNP calling with Agilent 50Mb target enrichment I am trying (and failing) to call SNPs using a reference file (.BED) specifically for the Agilent 50Mb Sureselect enrichment sequencing. I am using the GATK UnifiedGenotyper with the following commands. Any ideas? Thanks! java -jar ~/Sting/dist/GenomeAnalysisTK.jar \ -R ~/Documents/refFASTA/SureSelect_All_Exon_50mb.bed \ -l INFO \ -T UnifiedGenotyper \ -I ~/Documents/next_gen/sorted.N.dupesremoved.recali.bam \ -o ~/Documents/SNP/N_AgilentSS_50MB_gatk.vcf \ -stand_call_conf 50.0 \ -stand_emit_conf 10.0 \ -dcov 150

07-18-2011, 07:28 AM	#2
nullalleles Junior Member Location: Michigan Join Date: Jun 2011 Posts: 5	solved The above code should have contained the argument "-L" for the interval list (bed) file and also a "-R" for the reference fasta file!