Scripts used in article 'A simple pipeline for heteroplasmic variation detection of the mitochondrial genome from whole genome sequencing data'
Use $ git clone git@github.com:duanmq1994/Mitochondrial-variation-detection.git download those source codes or directly download the ZIP.
This step suggests that the users align the sequencing data against two references(MT.fasta and MT-8k.fatsa) respectively.
Then the .bam/.sam files need to be kept and used in the following steps.
Or users can creat their own 8k.fasta files using the fa8k.pl.
This script will creat a new .fasta file of mitochondrial genome to eliminate the influence on the head and tail reads because of a circular reference.
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Use the base_indel_count.pl.
This script will read the .bam/.sam file (use normal reference and 8k reference respectively) which has been sorted by SAMtools, then output two files: base-count.tsv and indel-count.tsv. -
Use the 1_8k_merge.pl to merge those two sets of .tsv files.
This step also needs users to creat the following results files using .bam/.sam files from two reference.
- Use the sequences_of_linkages.pl. This script will use the .bam/.sam file which aligned against two reference from heteroplasmic variation detection step. It will creat a primary id-variation.tsv file (intermediate result, should be sorted by sequence_id row).
- Use the variations_merge.pl to get the linkages-count.tsv file.
- Use the linkage_classify.pl.
This script will read the linkages-count.tsv file and output three kinds of linkage files: indels-linkage.tsv, indel-point_variations-linkage.tsv and point-variations.tsv.