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Old 07-12-2011, 12:22 PM   #1
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Location: Michigan

Join Date: Jun 2011
Posts: 5
Default 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
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Old 07-18-2011, 07:28 AM   #2
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Location: Michigan

Join Date: Jun 2011
Posts: 5
Default 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!
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agilent, gatk, snp, sureselect, unifiedgenotyper

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