python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL11A.PE.a.bam SAMstats-SPL11A.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL11B.PE.a.bam SAMstats-SPL11B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL12B.PE.a.bam SAMstats-SPL12B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL13A.PE.a.bam SAMstats-SPL13A.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL13B.PE.a.bam SAMstats-SPL13B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL13D.PE.a.bam SAMstats-SPL13D.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL14B.PE.a.bam SAMstats-SPL14B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL15A.PE.a.bam SAMstats-SPL15A.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL15B.PE.a.bam SAMstats-SPL15B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL15D.PE.a.bam SAMstats-SPL15D.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL16A.PE.a.bam SAMstats-SPL16A.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL16D.PE.a.bam SAMstats-SPL16D.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL18A.PE.a.bam SAMstats-SPL18A.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL18D2.PE.a.bam SAMstats-SPL18D2.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL19B_rep1.PE.a.bam SAMstats-SPL19B_rep1.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL19B_rep2.PE.a.bam SAMstats-SPL19B_rep2.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL1D_rep1.PE.a.bam SAMstats-SPL1D_rep1.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL1D_rep2.PE.a.bam SAMstats-SPL1D_rep2.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL2A_rep1.PE.a.bam SAMstats-SPL2A_rep1.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL2A_rep2.PE.a.bam SAMstats-SPL2A_rep2.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL2B.PE.a.bam SAMstats-SPL2B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL2D.PE.a.bam SAMstats-SPL2D.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL3A.PE.a.bam SAMstats-SPL3A.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL3B.PE.a.bam SAMstats-SPL3B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL3D.PE.a.bam SAMstats-SPL3D.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL4A.PE.a.bam SAMstats-SPL4A.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL4B.PE.a.bam SAMstats-SPL4B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL4D.PE.a.bam SAMstats-SPL4D.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL5A.PE.a.bam SAMstats-SPL5A.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL5B.PE.a.bam SAMstats-SPL5B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL5D.PE.a.bam SAMstats-SPL5D.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL6A_rep1.PE.a.bam SAMstats-SPL6A_rep1.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL6A_rep2.PE.a.bam SAMstats-SPL6A_rep2.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL6B.PE.a.bam SAMstats-SPL6B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL6D.PE.a.bam SAMstats-SPL6D.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL7A.PE.a.bam SAMstats-SPL7A.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL7B.PE.a.bam SAMstats-SPL7B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL7D.PE.a.bam SAMstats-SPL7D.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL8A_rep1.PE.a.bam SAMstats-SPL8A_rep1.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL8A_rep2.PE.a.bam SAMstats-SPL8A_rep2.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL8B.PE.a.bam SAMstats-SPL8B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL8D1.PE.a.bam SAMstats-SPL8D1.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL9A_rep1.PE.a.bam SAMstats-SPL9A_rep1.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL9A_rep2.PE.a.bam SAMstats-SPL9A_rep2.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL9B.PE.a.bam SAMstats-SPL9B.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py SPL9D.PE.a.bam SAMstats-SPL9D.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Ta-input.PE.a.bam SAMstats-Ta-input.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo
python /oak/stanford/groups/akundaje/marinovg/code/SAMstats.py Ta-input2.PE.a.bam SAMstats-Ta-input2.PE.a -bam /oak/stanford/groups/akundaje/marinovg/genomes/Land_plants/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1/Triticum_aestivum-IWGSC_CS_RefSeq_v2.1.chrom.sizes /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools -paired -noNHinfo