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BaseVar: A python software for calling variants from ultra low pass WGS data.

Project description

Call variants from ultra low-pass WGS data.

Installation

pip install basevar

Quick start

Call variants from several bamfiles

basevar basetype -R reference.fasta \
    --regions chr11:5246595-5248428,chr17:41197764-41276135 \
    --batch-count 50 \
    -I 00alzqq6jw.bam \
    -I 09t3r9n2rg.bam \
    -I 0fkpl1p55b.bam \
    -I 13dg1gvsfk.bam \
    -I 17phildszl.bam \
    -I 1dbpgqt0dq.bam \
    -I 1kyws27hoc.bam \
    --output-vcf test.vcf.gz \
    --output-cvg test.cvg.tsv.gz \
    --nCPU 4 && echo "** 5 done **"

Or call variants from bamlist

basevar basetype -R reference.fasta \
    --regions chr11:5246595-5248428,chr17:41197764-41276135 \
    --batch-count 50 \
    -L bamfile.list \
    --output-vcf test.vcf.gz \
    --output-cvg test.cvg.tsv.gz \
    --nCPU 4 && echo "** 5 done **"

Project details


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