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-   -   GATK UnifiedGenotyper SNP calling with Agilent 50Mb target enrichment (http://seqanswers.com/forums/showthread.php?t=12675)

nullalleles 07-12-2011 12:22 PM

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

nullalleles 07-18-2011 07:28 AM

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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