#!/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/ATAC/HG00621/MatReads1_A.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG00621_Mat_A_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG00621_A_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG00621/PatReads1_A.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG00621_Pat_A_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG00621_A_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG00621/MatReads1_B.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG00621_Mat_B_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG00621_B_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG00621/PatReads1_B.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG00621_Pat_B_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG00621_B_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG00741/MatReads1_A.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG00741_Mat_A_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG00741_A_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG00741/PatReads1_A.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG00741_Pat_A_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG00741_A_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG00741/MatReads1_B.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG00741_Mat_B_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG00741_B_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG00741/PatReads1_B.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG00741_Pat_B_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG00741_B_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG01952/MatReads1_A.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG01952_Mat_A_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG01952_A_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG01952/PatReads1_A.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG01952_Pat_A_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG01952_A_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG01952/MatReads1_B.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG01952_Mat_B_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG01952_B_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG01952/PatReads1_B.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG01952_Pat_B_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG01952_B_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG01978/MatReads1_A.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG01978_Mat_A_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG01978_A_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG01978/PatReads1_A.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG01978_Pat_A_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG01978_A_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG01978/MatReads1_B.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG01978_Mat_B_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG01978_B_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG01978/PatReads1_B.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG01978_Pat_B_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG01978_B_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG03516/MatReads1_A.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG03516_Mat_A_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG03516_A_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG03516/PatReads1_A.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG03516_Pat_A_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG03516_A_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG03516/MatReads1_B.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG03516_Mat_B_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG03516_B_CHM13.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/ATAC/HG03516/PatReads1_B.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/ATAC/HG03516_Pat_B_CHM13_phased_ATAC.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/ATACseq_CHM13_alignments/step2.1_trimed_HG03516_B_CHM13.bam