linkage-analysis~single-cell_CellRanger-VarTrix

input_1:10x CNV reads (file names must be like SampleName_S1_L001_R1_001.fastq.gz)

input_1/input_S1_L001_R1_001.fastq.gz

input_1/input_S1_L001_R2_001.fastq.gz

input_1/input_S1_L002_R1_001.fastq.gz

input_1/input_S1_L002_R2_001.fastq.gz

input_1/input_S1_L003_R1_001.fastq.gz

input_1/input_S1_L003_R2_001.fastq.gz

input_1/input_S1_L004_R1_001.fastq.gz

input_1/input_S1_L004_R2_001.fastq.gz

input_1/input_S1_L005_R1_001.fastq.gz

input_1/input_S1_L005_R2_001.fastq.gz

input_2:A reference genome file

input_2/scaffolds.fa

input_3:The 10x Cell Ranger DNA - 1.1.0 software file (download from https

Command

Output

pseudochr.re.fa.removedup.matrix.clean.txt_clean.txt

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	dummy	AAACGGGAGCGTTGCC-1	AAACGGGAGGATCGCA-1	AAACGGGCACGCTGAC-1	AAAGATGAGAAACCCG-1	AAAGATGTCAGGTACT-1	AAAGCAACATCCTGGG-1	AAAGCAAGTTCTGTCC-1	AAAGTAGAGGAGTTGC-1	AAAGTAGAGGCATGGT-1	AAAGTAGTCATCACTT-1	AAATGCCCAAGGCTAG-1	AAATGCCTCCGGCTAG-1	AACACGTCATCAGCAT-1	AACCATGGTTGCCAAT-1	AACGTTGTCCAGGAAG-1	AACTCAGGTATGACTC-1	AACTCAGGTGGCAACA-1	AACTCCCTCACACCTC-1	AACTCCCTCATCGGTA-1	AACTCTTCACGACGCT-1	AACTCTTTCCTAGACA-1	AACTGGTAGCAGATCG-1	AACTGGTCATGGGCCT-1	AACTGGTGTTTCCGAA-1	AACTTTCAGGAGTCTG-1	AAGACCTTCAATCTTC-1	AAGCCGCCACTATGCA-1	AAGCCGCCATCTCACC-1	AAGCCGCCATGGATTC-1	AAGGAGCAGGGTTCGA-1	AAGGAGCCATGCCGCA-1	AAGGAGCTCGCGGACT-1	AAGGCAGCAGAACCAG-1	AAGGTTCTCCTCTGCA-1	AAGTCTGGTTGCGGCT-1	AATCCAGAGCAAATCA-1	AATCCAGCAAACCCTA-1	AATCCAGCACGGCTGT-1	AATCGGTAGAAACGCC-1	AATCGGTTCCACTGCT-1	ACACCAACAAGGCCCT-1	ACACCAAGTGTTCCGG-1	ACACCCTTCAGCGGCT-1	ACACCGGGTGTTACGT-1	ACACCGGTCATGTGAC-1	ACACTGATCCAGGCGT-1	ACACTGATCCCAAAGT-1	ACAGCTAAGCCATGCC-1	ACATGGTCAAATAGGT-1	ACATGGTCAGTGTGGA-1	ACATGGTTCTATGCAG-1	ACCGTAAAGGGTTCCC-1	ACCGTAAAGTCGTACT-1	ACCGTAACACCCGTTT-1	ACCGTAACACGTCGGT-1	ACCGTAATCAAAGTGA-1	ACGAGCCGTCAGTGGA-1	ACGAGCCTCCACTGCT-1	ACGAGGACATAACAAG-1	ACGAGGACATGAGAAT-1	ACGATACGTGCTGTAT-1	ACGATGTCAACTCGCG-1	ACGATGTGTCCGGTTG-1	ACGCAGCCATTTAGGC-1	ACGCCAGCAACCGCTG-1	ACGCCAGCATACTGCA-1	ACGCCAGTCGAGCACC-1	ACGCCAGTCGTTCAAG-1	ACGCCGACAAGCAAGC-1	ACGGAGAAGGCCCTCA-1	ACGGCCACAGGGAAGG-1	ACGGCCATCAATCTTC-1	ACGGCCATCGAGAGGT-1	ACGGGCTAGAAGGTGA-1	ACGGGCTAGTCCGGTC-1	ACGGGCTAGTCTCCTC-1	ACGGGCTGTGAGTCAG-1	ACGGGTCAGCTTTCAG-1	ACGGGTCAGGGAACGG-1	ACTATCTAGAATTCCC-1	ACTATCTGTACCAACT-1	ACTGAACTCGTTACCC-1	ACTGAGTGTTCTCAAG-1	ACTGATGCAGCTTGAT-1	ACTGCTCTCCGCTTGT-1	ACTGTCCAGTCATCCA-1	ACTGTCCGTAACTGTC-1	ACTTACTGTCCTCCAT-1	ACTTACTGTGTAACCT-1	ACTTACTTCATCGACA-1	AGAATAGAGTACGCGA-1	AGAATAGTCCACAGAT-1	AGAATAGTCGTGTCAA-1	AGAGCGAAGGTGCACA-1	AGATCTGGTGAAGCCA-1	AGATTGCCAACCCTGG-1	AGCAGCCAGAGCCCAA-1	AGCCTAAGTCAACTCA-1	AGCGGTCCATTCTTCA-1	AGCTCCTCACTTTCCG-1	AGCTCTCAGCGATGAC-1	AGCTCTCGTCCCTGGA-1	AGCTTGAAGGTCGGAT-1	AGGCCACTCCGCGAGT-1	AGGCCGTAGGTACTCT-1	AGGCCGTCAGTTATGC-1	AGGCCGTCATGAGGCA-1	AGGCCGTGTTGTCGCG-1	AGGCCGTTCGGATCCG-1	AGGCCGTTCTTCACGC-1	AGGGAGTAGGAAACTT-1	AGGGAGTCAAGAACTA-1	AGGGAGTGTAACGGCA-1	AGGGATGAGAAGGTGA-1	AGGTCATCAGACGAGT-1	AGGTCATTCGGATGCC-1	AGGTCCGAGTCCATAC-1	AGGTCCGTCCACTTCG-1	AGTGAGGAGGACCAGT-1	AGTGAGGAGTAGCCGA-1	AGTGAGGTCATCTCCG-1	AGTGGGAGTGAACTCT-1	AGTGTCAAGACTGGCA-1	AGTGTCAAGATCCTGT-1	AGTGTCAGTTCTGTCC-1	AGTTGGTAGGACCACA-1	AGTTGGTTCAACAGTC-1	ATAACGCAGAAGGCCT-1	ATAAGAGAGATACACA-1	ATAAGAGAGCAGAGAA-1	ATAAGAGGTCTCGAGC-1	ATAGACCGTAATCAGA-1	ATAGACCTCGACCCTT-1	ATCACGACAAATAGGT-1	ATCACGACAAGCTACT-1	ATCACGAGTGAGTCAG-1	ATCACGATCAGTAAAG-1	ATCATCTGTTGCCAAT-1	ATCCGAATCCTCATCG-1	ATCTACTGTGACATCT-1	ATCTACTTCAGAGTCT-1	ATCTGCCGTCCTCCAT-1	ATGCGATAGGCTCTCG-1	ATGCGATGTTGCACTA-1	ATGCGATTCGTGTACA-1	ATGCGATTCTTTCGTA-1	ATGGGAGTCAGTACAC-1	ATGGGAGTCCGCGACA-1	ATGTGTGTCGAGCCGT-1	ATTACTCCACCACATA-1	ATTACTCGTCAACATC-1	ATTATCCTCGGCTCAG-1	ATTATCCTCGTTGGAT-1	ATTCTACAGGAGTTGC-1	ATTCTACCATCGCACG-1	ATT

pseudochr.re.fa.removedup.matrix.clean.txt.vcf2.family

dummy	AAACGGGAGCGTTGCC-1	AAACGGGAGGATCGCA-1	AAACGGGCACGCTGAC-1	AAAGATGAGAAACCCG-1	AAAGATGTCAGGTACT-1	AAAGCAACATCCTGGG-1	AAAGCAAGTTCTGTCC-1	AAAGTAGAGGAGTTGC-1	AAAGTAGAGGCATGGT-1	AAAGTAGTCATCACTT-1	AAATGCCCAAGGCTAG-1	AAATGCCTCCGGCTAG-1	AACACGTCATCAGCAT-1	AACCATGGTTGCCAAT-1	AACGTTGTCCAGGAAG-1	AACTCAGGTATGACTC-1	AACTCAGGTGGCAACA-1	AACTCCCTCACACCTC-1	AACTCCCTCATCGGTA-1	AACTCTTCACGACGCT-1	AACTCTTTCCTAGACA-1	AACTGGTAGCAGATCG-1	AACTGGTCATGGGCCT-1	AACTGGTGTTTCCGAA-1	AACTTTCAGGAGTCTG-1	AAGACCTTCAATCTTC-1	AAGCCGCCACTATGCA-1	AAGCCGCCATCTCACC-1	AAGCCGCCATGGATTC-1	AAGGAGCAGGGTTCGA-1	AAGGAGCCATGCCGCA-1	AAGGAGCTCGCGGACT-1	AAGGCAGCAGAACCAG-1	AAGGTTCTCCTCTGCA-1	AAGTCTGGTTGCGGCT-1	AATCCAGAGCAAATCA-1	AATCCAGCAAACCCTA-1	AATCCAGCACGGCTGT-1	AATCGGTAGAAACGCC-1	AATCGGTTCCACTGCT-1	ACACCAACAAGGCCCT-1	ACACCAAGTGTTCCGG-1	ACACCCTTCAGCGGCT-1	ACACCGGGTGTTACGT-1	ACACCGGTCATGTGAC-1	ACACTGATCCAGGCGT-1	ACACTGATCCCAAAGT-1	ACAGCTAAGCCATGCC-1	ACATGGTCAAATAGGT-1	ACATGGTCAGTGTGGA-1	ACATGGTTCTATGCAG-1	ACCGTAAAGGGTTCCC-1	ACCGTAAAGTCGTACT-1	ACCGTAACACCCGTTT-1	ACCGTAACACGTCGGT-1	ACCGTAATCAAAGTGA-1	ACGAGCCGTCAGTGGA-1	ACGAGCCTCCACTGCT-1	ACGAGGACATAACAAG-1	ACGAGGACATGAGAAT-1	ACGATACGTGCTGTAT-1	ACGATGTCAACTCGCG-1	ACGATGTGTCCGGTTG-1	ACGCAGCCATTTAGGC-1	ACGCCAGCAACCGCTG-1	ACGCCAGCATACTGCA-1	ACGCCAGTCGAGCACC-1	ACGCCAGTCGTTCAAG-1	ACGCCGACAAGCAAGC-1	ACGGAGAAGGCCCTCA-1	ACGGCCACAGGGAAGG-1	ACGGCCATCAATCTTC-1	ACGGCCATCGAGAGGT-1	ACGGGCTAGAAGGTGA-1	ACGGGCTAGTCCGGTC-1	ACGGGCTAGTCTCCTC-1	ACGGGCTGTGAGTCAG-1	ACGGGTCAGCTTTCAG-1	ACGGGTCAGGGAACGG-1	ACTATCTAGAATTCCC-1	ACTATCTGTACCAACT-1	ACTGAACTCGTTACCC-1	ACTGAGTGTTCTCAAG-1	ACTGATGCAGCTTGAT-1	ACTGCTCTCCGCTTGT-1	ACTGTCCAGTCATCCA-1	ACTGTCCGTAACTGTC-1	ACTTACTGTCCTCCAT-1	ACTTACTGTGTAACCT-1	ACTTACTTCATCGACA-1	AGAATAGAGTACGCGA-1	AGAATAGTCCACAGAT-1	AGAATAGTCGTGTCAA-1	AGAGCGAAGGTGCACA-1	AGATCTGGTGAAGCCA-1	AGATTGCCAACCCTGG-1	AGCAGCCAGAGCCCAA-1	AGCCTAAGTCAACTCA-1	AGCGGTCCATTCTTCA-1	AGCTCCTCACTTTCCG-1	AGCTCTCAGCGATGAC-1	AGCTCTCGTCCCTGGA-1	AGCTTGAAGGTCGGAT-1	AGGCCACTCCGCGAGT-1	AGGCCGTAGGTACTCT-1	AGGCCGTCAGTTATGC-1	AGGCCGTCATGAGGCA-1	AGGCCGTGTTGTCGCG-1	AGGCCGTTCGGATCCG-1	AGGCCGTTCTTCACGC-1	AGGGAGTAGGAAACTT-1	AGGGAGTCAAGAACTA-1	AGGGAGTGTAACGGCA-1	AGGGATGAGAAGGTGA-1	AGGTCATCAGACGAGT-1	AGGTCATTCGGATGCC-1	AGGTCCGAGTCCATAC-1	AGGTCCGTCCACTTCG-1	AGTGAGGAGGACCAGT-1	AGTGAGGAGTAGCCGA-1	AGTGAGGTCATCTCCG-1	AGTGGGAGTGAACTCT-1	AGTGTCAAGACTGGCA-1	AGTGTCAAGATCCTGT-1	AGTGTCAGTTCTGTCC-1	AGTTGGTAGGACCACA-1	AGTTGGTTCAACAGTC-1	ATAACGCAGAAGGCCT-1	ATAAGAGAGATACACA-1	ATAAGAGAGCAGAGAA-1	ATAAGAGGTCTCGAGC-1	ATAGACCGTAATCAGA-1	ATAGACCTCGACCCTT-1	ATCACGACAAATAGGT-1	ATCACGACAAGCTACT-1	ATCACGAGTGAGTCAG-1	ATCACGATCAGTAAAG-1	ATCATCTGTTGCCAAT-1	ATCCGAATCCTCATCG-1	ATCTACTGTGACATCT-1	ATCTACTTCAGAGTCT-1	ATCTGCCGTCCTCCAT-1	ATGCGATAGGCTCTCG-1	ATGCGATGTTGCACTA-1	ATGCGATTCGTGTACA-1	ATGCGATTCTTTCGTA-1	ATGGGAGTCAGTACAC-1	ATGGGAGTCCGCGACA-1	ATGTGTGTCGAGCCGT-1	ATTACTCCACCACATA-1	ATTACTCGTCAACATC-1	ATTATCCTCGGCTCAG-1	ATTATCCTCGTTGGAT-1	ATTCTACAGGAGTTGC-1	ATTCTACCATCGCACG-1	ATTGGACAGGCCCACT-1	ATTGGACCAGACGAAC-1	ATTGGTGAGTC

Log