For Docker Users
Basic usage(required):
summer --MODE -i <INPUTDIR> -s <SAMPLEFILE> -o <OUTDIR> -rd <REFDIR> -r <REFFILE> -x {male,female}
Example:
summer --align -i /data/project/ -s sample.fastq -o /data/output/ -rd /data/refseqdir -r hg38.fa -x male
Explanation for options:
-h, --help show this help message and exit
-v, --version show program's version number and exit
-i , --inputdir INPUT Input directory and file name, Fasta, Fastq, or gz files.
-s, --samplefile SAMPLE Input file name, Fasta, Fastq, gz ,or .bam, .vcf files.
-o, --outdir OUTDIR Position of output directionary
-rd, --refdir REFDIR The position of the reference genome.
-r, --ref REF The reference file will be used to align reads to, filename. Hg38 is recommended.
-x, --sex {male,female} Biological sex of the sample, male or female.
-t, --thread THREAD Number of threads being used (default: 6)
--hpo One or several HPO standarized phenotypes of the sample, e.g., --hpo HP:0001250 --hpo HP:0031936
-c, --Caller {cutesv,sniffles2,svim,combined} In case if you want to choose specific caller otherwise default will be used. (default: sniffles)
You may also feel free to enter a container by:
docker run -it chuhongyuan/summer:latest
And then use any software you need.
MODEs of SUMMER
summer --all:
This command will run all the summer pipeline, as following:
Identity STRs in the whole genome
summer --align:
This command align the reads using minimap2, then index and sort the bam using samtools.
#Bascial Usage
summer --align -i <INPUTDIR> -s <SAMPLEFILE> -o <OUTDIR> -rd <REFDIR> -r <REFFILE> -x {male,female}
#Example
summer --align -i /data/project/ -s sample.fastq -o /data/output/ -rd /data/refseqdir -r hg38.fa -x male
summer --pandepth:
This command will evaluate sequencing quality based on bam files using pandepth.
#Bascial Usage
summer --pandepth -i <INPUTDIR> -s <SAMPLEFILE> -o <OUTDIR> -rd <REFDIR> -r <REFFILE> -x {male,female}
#Example
summer --pandepth -i /data/project/ -s sample_align_sorted.bam -o /data/output/ -rd /data/refseqdir -r hg38.fa -x male
summer --snv:
This command will detecte SNVs from bam files using clair3.
#Bascial Usage
summer --snv -i <INPUTDIR> -s <SAMPLEFILE> -o <OUTDIR> -rd <REFDIR> -r <REFFILE> -x {male,female}
#Example
summer --snv -i /data/project/ -s sample_align_sorted.bam -o /data/output/ -rd /data/refseqdir -r hg38.fa -x male
summer --sv:
This command will detecte SVs from bam files using the software you choose. Input should be sorted bam.
#Bascial Usage
summer --sv -i <INPUTDIR> -s <SAMPLEFILE> -o <OUTDIR> -rd <REFDIR> -r <REFFILE> -x {male,female}
#Example
summer --sv -i /data/project/ -s sample_align_sorted.bam -o /data/output/ -rd /data/refseqdir -r hg38.fa -x male
summer --svanna:
This command will annote the SVs using svanna.
#Bascial Usage
summer --svanna -i <INPUTDIR> -s <SAMPLEFILE> -o <OUTDIR> -rd <REFDIR> -r <REFFILE> -x {male,female} --hpo HP:XXXXXXX
#Example
summer --svanna -i /data/project/ -s combisv_handled.vcf -o /data/output/ -rd /data/refseqdir -r hg38.fa -x male --hpo HP:0001250 --hpo:HP0001263
summer --mobile_element_detection_mode:
This command will detecte Mobile Elements from bam files using tldr.
#Bascial Usage
summer --mobile_element_detection_mode -i <INPUTDIR> -s <SAMPLEFILE> -o <OUTDIR> -rd <REFDIR> -r <REFFILE> -x {male,female}
#Example
summer --mobile_element_detection_mode -i /data/project/ -s sample_align_sorted.bam -o /data/output/ -rd /data/refseqdir -r hg38.fa -x male
summer --WGSstr:
This command will detecte whole genome Tandom Repeats from bam files using straglr.
#Bascial Usage
summer --WGSstr -i <INPUTDIR> -s <SAMPLEFILE> -o <OUTDIR> -rd <REFDIR> -r <REFFILE> -x {male,female}
#Example
summer --WGSstr -i /data/project/ -s sample_align_sorted.bam -o /data/output/ -rd /data/refseqdir -r hg38.fa -x male
summer --str:
This command will detecte Tandom Repeats from bam files using straglr. In case when using targeted ONT long-sequencing.
#Bascial Usage
summer --str -i <INPUTDIR> -s <SAMPLEFILE> -o <OUTDIR> -rd <REFDIR> -r <REFFILE> -x {male,female}
#Example
summer --str -i /data/project/ -s sample_targeted_align_sorted.bam -o /data/output/ -rd /data/refseqdir -r hg38.fa -x male
#Please make sure your targeted file contain at least 1 known repeat region associated disorder~
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