├── LICENSE ├── README.md ├── ScanIndel.py ├── example ├── README ├── input_data │ ├── config.txt │ ├── sample.txt │ ├── test.read1.fq │ └── test.read2.fq ├── output_example │ ├── test.assembly.indel.vcf │ ├── test.mapping.indel.vcf │ └── test.merged.indel.vcf └── run_scanindel.sh └── tools ├── inchworm └── vcf-combine.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/README.md -------------------------------------------------------------------------------- /ScanIndel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/ScanIndel.py -------------------------------------------------------------------------------- /example/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/example/README -------------------------------------------------------------------------------- /example/input_data/config.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/example/input_data/config.txt -------------------------------------------------------------------------------- /example/input_data/sample.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/example/input_data/sample.txt -------------------------------------------------------------------------------- /example/input_data/test.read1.fq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/example/input_data/test.read1.fq -------------------------------------------------------------------------------- /example/input_data/test.read2.fq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/example/input_data/test.read2.fq -------------------------------------------------------------------------------- /example/output_example/test.assembly.indel.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/example/output_example/test.assembly.indel.vcf -------------------------------------------------------------------------------- /example/output_example/test.mapping.indel.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/example/output_example/test.mapping.indel.vcf -------------------------------------------------------------------------------- /example/output_example/test.merged.indel.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/example/output_example/test.merged.indel.vcf -------------------------------------------------------------------------------- /example/run_scanindel.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/example/run_scanindel.sh -------------------------------------------------------------------------------- /tools/inchworm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/tools/inchworm -------------------------------------------------------------------------------- /tools/vcf-combine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cauyrd/ScanIndel/HEAD/tools/vcf-combine.py --------------------------------------------------------------------------------