#!/bin/bash
#SBATCH --mem=32G
#SBATCH --mail-type=ALL
#SBATCH --mail-user=n.a.tekkey@wustl.edu

eval $( spack load --sh samtools@1.13)

samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG00621/Dataset_1/MatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG00621_Mat_A_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG00621_1.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG00621/Dataset_1/PatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG00621_Pat_A_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG00621_1.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG00621/Dataset_2/MatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG00621_Mat_B_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG00621_2.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG00621/Dataset_2/PatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG00621_Pat_B_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG00621_2.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG00741/Dataset_1/MatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG00741_Mat_A_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG00741_1.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG00741/Dataset_1/PatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG00741_Pat_A_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG00741_1.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG00741/Dataset_2/MatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG00741_Mat_B_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG00741_2.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG00741/Dataset_2/PatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG00741_Pat_B_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG00741_2.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG01952/Dataset_1/MatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG01952_Mat_A_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG01952_1.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG01952/Dataset_1/PatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG01952_Pat_A_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG01952_1.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG01952/Dataset_2/MatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG01952_Mat_B_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG01952_2.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG01952/Dataset_2/PatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG01952_Pat_B_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG01952_2.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG01978/Dataset_1/MatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG01978_Mat_A_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG01978_1.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG01978/Dataset_1/PatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG01978_Pat_A_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG01978_1.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG01978/Dataset_2/MatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG01978_Mat_B_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG01978_2.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG01978/Dataset_2/PatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG01978_Pat_B_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG01978_2.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG03516/Dataset_1/MatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG03516_Mat_A_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG03516_1.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG03516/Dataset_1/PatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG03516_Pat_A_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG03516_1.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG03516/Dataset_2/MatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG03516_Mat_B_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG03516_2.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/RNA/HG03516/Dataset_2/PatReads1_1.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/RNA/HG03516_Pat_B_CHM13_phased_RNA.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/RNA-seq_alignments/HG03516_2.CHM13v2.0.gencode_v29/align/rep1PE_unstranded_genome.bam