basevar 0.0.1.3
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Description:
basevar 0.0.1.3
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 **"
License:
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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