From: http://biostar.stackexchange.com/questions/1269/what-is-the-best-pipeline-for-human-whole-exome-sequencing
/bin/BWA/bwa aln -f /output/FOO.sai -t 3 /seq/REFERENCE/human_18.fasta /seq/FQ/FOO.sanger.fq
/bin/BWA/bwa samse -f /output/FOO.sam /seq/REFERENCE/human_18.fasta /output/FOO.sai /seq/FQ/FOO.sanger.fq
/bin/SAMTOOLS/samtools import /seq/REFERENCE/human_18.fasta /output/FOO.sam /output/FOO.bam
/bin/SAMTOOLS/samtools sort /output/FOO.bam /output/FOO.sorted
/bin/SAMTOOLS/samtools index /output/FOO.sorted.bam /output/FOO.sorted.bam.bai
java -jar /bin/GTK/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /seq/REFERENCE/human_18.fasta -I /output/FOO.sorted.bam  -o /output/FOO.intervals
java -jar /bin/GTK/GenomeAnalysisTK.jar -T IndelRealigner -R /seq/REFERENCE/human_18.fasta -I /output/FOO.sorted.bam -targetIntervals /output/FOO.intervals --output /output/FOO.sorted.realigned.bam
(optional: samtools calmd -Abr FOO.sorted.bam human_18.fasta > FOO.baq.bam)
/bin/SAMTOOLS/samtools index /output/FOO.sorted.realigned.bam /output/FOO.sorted.realigned.bam.bai
java -jar /bin/GTK/GenomeAnalysisTK.jar -T IndelGenotyperV2 -R /seq/REFERENCE/human_18.fasta -I /output/FOO.sorted.realigned.bam -O /output/FOO_indel.txt --verbose -o /output/FOO_indel_statistics.txt
java -jar /bin/GTK/GenomeAnalysisTK.jar -T UnifiedGenotyper -R /seq/REFERENCE/human_18.fasta -I /output/FOO.sorted.realigned.bam -varout /output/FOO.geli.calls -vf GELI -stand_call_conf 30.0 -stand_emit_conf 10.0 -pl SOLEXA
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