Usage¶

Required arguments¶

-d –-DIR    Directory path of the .BAM files
or
-l --List   A file with the list of files ( The form is referred above in the 'Input' section )

-r --Ref    Reference file


Additionally for the Targeted sequencing dataset

-b --BEDfile    Targeted bed file for targeted sequencing data mode.

Optional arguments¶

-v –-RefVer ['hg38','hg19']. Default is "hg38". If the reference is hg19, give this option ‘-r hg19’.

-o --OutputDIR  Output directory path. BAMixChecker creates the new directory '/BAMixChecker' under the current directory as a default.

-p --MaxProcess The max number of process. Default = 1

--FullPATH  Used to report the full path of the file. BAMixChecker otherwise reports only the file name as a default.

--RemoveVCF Use this option to remove called VCF files after running.

--OFFFileNameMatching   Use this option to compare files only by genotype.

-nhSNP --NonHumanSNPlist    A SNP list for non-human organism sample matching check-up.

-pld' --Ploidy  Ploidy of sample. Default = 2 for human.

Usage for each data type¶

BAMixChecker runs a mode for WES and RNA-seq as a default without bed file.

If a BED file is given using the -b option, it runs as a targeted sequencing mode.

WGS or WES or RNA-Seq data

$ python BAMixChecker.py \
-d /path/aligned/files/ \
-r /path/reference/HG38/genome.fa \
-o /path/new/directory

Or

$ python BAMixChecker.py \
-l /path/aligned/file_list.txt \
-p 4 \
-r /path/reference/HG38/genome.fa \
-o /path/new/directory

Targeted sequencing data

$ python BAMixChecker.py \
-d /path/aligned/files/ \
-p 2 \
-r /path/reference/HG19/genome.fa \
-o /path/new/directory \
-v hg19 \
-b /path/targeted.bed

Or

$ python BAMixChecker.py \
-l /path/aligned/file_list.txt \
-r /path/reference/HG19/genome.fa \
-o /path/new/directory \
-v hg19 \
-b /path/targeted.bed

Note

If the dataset consists of both WES/RNA-Seq and Targeted sequencing data, all using the same reference, run as Targeted sequencing data mode with the targeted bed file for the Targeted sequencing data and give both types of BAM files at once.

Tutorial¶

Set the required variables:

$ cd BAMixChecker/tutorialData
$ vim script_example.sh

    BAMixChecker_PATH=/path/to/BAMixChecker
    OUT_DIR=/output/dir
    REF=/path/of/reference/hg38/genome.fa

Run the script:
```
$ sh script_example.sh
```