RUNNING: /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/FreeBayes/broadinstitute.org/cancer.genome.analysis/11166/2//speedseq/bin/speedseq somatic -o 160413_10x_sim -t 2 -v /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam
Sourcing executables from /xchip/tcga/gdac_prod/applications/process_mgmt/firehose_task_registry/cga/FreeBayes/broadinstitute.org/cancer.genome.analysis/11166/2//speedseq/bin/speedseq.config ...
Calling somatic variants...

        create temporary directory

        /xchip/gistic/Jeremiah/GIT/speedseq//bin/sambamba view -H /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam | grep "^@SQ" | cut -f 2- | awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' > 160413_10x_sim.L31xIbohEMvJ/windows.bed

        /xchip/gistic/Jeremiah/GIT/speedseq//bin/freebayes -f /seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta \
            --pooled-discrete \
            --min-repeat-entropy 1 \
            --genotype-qualities \
            --min-alternate-fraction 0.05 \
            --min-alternate-count 2 \
            --region $chrom:$start..$end \
            /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/normfull_0.6_subsampled.bam /xchip/gistic/Jeremiah/Projects/SnowmanPaper/Benchmark/160410/sim_wnormal_10x_d1.rh.bam \
            | somatic_filter 1e-5 18 0 \
            > 160413_10x_sim.L31xIbohEMvJ/160413_10x_sim.$chrom:$start..$end.vcf

        cat 160413_10x_sim.L31xIbohEMvJ/var_command.txt | /xchip/gistic/Jeremiah/GIT/speedseq//bin/parallel -j 2

        grep "^##" 160413_10x_sim.L31xIbohEMvJ/160413_10x_sim.1:0..249250621.vcf \
        | cat - <(echo '##INFO=<ID=SSC,Number=1,Type=Float,Description="Somatic score">') <(grep "^#CHROM" 160413_10x_sim.L31xIbohEMvJ/160413_10x_sim.1:0..249250621.vcf) > 160413_10x_sim.L31xIbohEMvJ/header.txt

        cat 160413_10x_sim.L31xIbohEMvJ/160413_10x_sim."$chrom:$start..$end".vcf | grep -v "^#" \
            | sort -k1,1 -k2,2n | cat 160413_10x_sim.L31xIbohEMvJ/header.txt - \
            | /xchip/gistic/Jeremiah/GIT/speedseq//bin/bgzip -c > 160413_10x_sim.vcf.gz

        /xchip/gistic/Jeremiah/GIT/speedseq//bin/tabix -f -p vcf 160413_10x_sim.vcf.gz
# Make PED file
echo -e "1\tHCC1143_BL\tNone\tNone\t0\t1\n1\ttumor_sim\tNone\tNone\t0\t2" > 160413_10x_sim.ped

        rm -r 160413_10x_sim.L31xIbohEMvJ
Done