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This is a repo with scripts to convert the output of VarScan to the VCF format.
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To install VarScan follow the intructions here and to execute it follow these intructions.
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To excute this script just run
python vscan_pileup2cns2vcf.py test_file.tsv > test_file.vcf -
Please note that the VCF file contains all positions, even those without variants, so it needs some cleaning afterwards. For further cleaning of the VCF please ran
vcf_cleaning.Rscript.
forked from mohammedkhalfan/Varscan2VCF
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Convert VarScan output to VCF format
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- Python 96.3%
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