#!/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/WGBS/HG00621/HG00621_CGGCTATGAT-ACTATAGCCT_mat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG00621_Mat_CGGCTATGAT-ACTATAGCCT_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HJLVHDSX2_CGGCTATGAT-ACTATAGCCT_L002_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG00621/HG00621_CGGCTATGAT-ACTATAGCCT_pat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG00621_Pat_CGGCTATGAT-ACTATAGCCT_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HJLVHDSX2_CGGCTATGAT-ACTATAGCCT_L002_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG00621/HG00621_TCCGCGAAAT-ACATAGAGGC_mat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG00621_Mat_TCCGCGAAAT-ACATAGAGGC_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HJLVHDSX2_TCCGCGAAAT-ACATAGAGGC_L002_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG00621/HG00621_TCCGCGAAAT-ACATAGAGGC_pat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG00621_Pat_TCCGCGAAAT-ACATAGAGGC_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HJLVHDSX2_TCCGCGAAAT-ACATAGAGGC_L002_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG00741/HG00741_ATTACTCGAT-ACATAGAGGC_mat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG00741_Mat_ATTACTCGAT-ACATAGAGGC_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HLMK7DSXY_ATTACTCGAT-ACATAGAGGC_L002_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG00741/HG00741_ATTACTCGAT-ACATAGAGGC_pat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG00741_Pat_ATTACTCGAT-ACATAGAGGC_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HLMK7DSXY_ATTACTCGAT-ACATAGAGGC_L002_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG00741/HG00741_ATTACTCGAT-ACTATAGCCT_mat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG00741_Mat_ATTACTCGAT-ACTATAGCCT_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HLMK7DSXY_ATTACTCGAT-ACTATAGCCT_L002_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG00741/HG00741_ATTACTCGAT-ACTATAGCCT_pat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG00741_Pat_ATTACTCGAT-ACTATAGCCT_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HLMK7DSXY_ATTACTCGAT-ACTATAGCCT_L002_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG01952/HG01952_CGGCTATGAT-ACCCTATCCT_mat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG01952_Mat_CGGCTATGAT-ACCCTATCCT_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HMMN5DSX2_CGGCTATGAT-ACCCTATCCT_L001_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG01952/HG01952_CGGCTATGAT-ACCCTATCCT_pat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG01952_Pat_CGGCTATGAT-ACCCTATCCT_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HMMN5DSX2_CGGCTATGAT-ACCCTATCCT_L001_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG01952/HG01952_TCCGCGAAAT-ACCCTATCCT_mat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG01952_Mat_TCCGCGAAAT-ACCCTATCCT_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HMM35DSX2_TCCGCGAAAT-ACCCTATCCT_L004_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG01952/HG01952_TCCGCGAAAT-ACCCTATCCT_pat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG01952_Pat_TCCGCGAAAT-ACCCTATCCT_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HMM35DSX2_TCCGCGAAAT-ACCCTATCCT_L004_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG01978/HG01978_CGGCTATGAT-ACATAGAGGC_mat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG01978_Mat_CGGCTATGAT-ACATAGAGGC_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HMM35DSX2_CGGCTATGAT-ACATAGAGGC_L004_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG01978/HG01978_CGGCTATGAT-ACATAGAGGC_pat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG01978_Pat_CGGCTATGAT-ACATAGAGGC_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HMM35DSX2_CGGCTATGAT-ACATAGAGGC_L004_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG01978/HG01978_TCCGCGAAAT-ACAGGCGAAG_mat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG01978_Mat_TCCGCGAAAT-ACAGGCGAAG_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HMMN5DSX2_TCCGCGAAAT-ACAGGCGAAG_L001_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG01978/HG01978_TCCGCGAAAT-ACAGGCGAAG_pat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG01978_Pat_TCCGCGAAAT-ACAGGCGAAG_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HMMN5DSX2_TCCGCGAAAT-ACAGGCGAAG_L001_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG03516/HG03516_TCCGCGAAAT-ACCAGGACGT_mat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG03516_Mat_TCCGCGAAAT-ACCAGGACGT_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HMMLNDSX2_TCCGCGAAAT-ACCAGGACGT_L003_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG03516/HG03516_TCCGCGAAAT-ACCAGGACGT_pat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG03516_Pat_TCCGCGAAAT-ACCAGGACGT_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HMMLNDSX2_TCCGCGAAAT-ACCAGGACGT_L003_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG03516/HG03516_TCCGCGAAAT-ACGTACTGAC_mat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG03516_Mat_TCCGCGAAAT-ACGTACTGAC_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HHYHLDSX2_TCCGCGAAAT-ACGTACTGAC_L002_bismark_bt2_pe.bam
samtools view -b --qname-file /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/WGBS/HG03516/HG03516_TCCGCGAAAT-ACGTACTGAC_pat.txt_sorted -o /scratch/twlab/tekkey/CellGenomicsRevisions/phasedReads/chm13PhasedAlign/WGBS/HG03516_Pat_TCCGCGAAAT-ACGTACTGAC_CHM13_phased_WGBS.bam  /scratch/hllab/Juan/Reference_Bias_Cell_Genomics_Revisions/WGBS_CHM13_alignments/2_bismark/HHYHLDSX2_TCCGCGAAAT-ACGTACTGAC_L002_bismark_bt2_pe.bam