karkinos

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Tumor genotyper, that detects SNV, absolute CNV and Tumor contents

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# About

karkinos is a tumor genotyper that detects single nucleotide variation (SNV)
and copy number variation (CNV) and calculates tumor cellularity from tumor-normal paired sequencing data.

Accurate CNV calling is achieved using continuous wavelet analysis and multi-state HMM,
while SNV call is adjusted by tumor cellularity and filtered by a heuristic filtering algorithm and Fisher Test.
Also, Noise calls in low depth regions are removed using the EM algorithm.

# Licence

Licensed under the Apache License, Version 2.0 (the &quot;License&quot;);
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an &quot;AS IS&quot; BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.

# Prerequisites

- git
- JDK >= 1.8 (Recommended 11)

# Build

```
$ git clone https://github.com/genome-rcast/karkinos.git
$ cd karkinos
$ ./gradlew uberjar
```

You don't need to install Gradle command.

`karkinos-standalone-X.Y.Z-SNAPSHOT.jar` is created in the `./build/libs/` directory.

# Required files

- BAM files for normal read alignment
- BAM files for tumor read alignment
- Capture target (BED format)
- dbSNP (See following for the file format)
- COSMIC (VCF format)
- `karkinos.property`

dbSNP file format is as follows:

1. bin (for indexing)
2. chromosome
3. start (0 based)
4. end (1 based)
5. rs#
6. score
7. strand
8. ref allele from NCBI
9. ref allele from UCSC
10. observed alleles
11. molType
12. class
13. valid
14. avHet
15. avHetSE
16. func
17. location type
18. weight
19. exceptions
20. submitterCount
21. submitters
22. allele frequency count
23. alleles
24. alleleNs
25. alleleFreqs
26. bitfields

e.g.

```
585	chr1	10468	10469	rs117577454	0	+	C	C	C/G	genomic	single	by-1000genomes	0	0	unknown	exact	1		1	1000GENOMES,	2	G,C,	18.000000,102.000000,	0.150000,0.850000,
```

# Run

The current version of karkinos supports only one subcommand, `analysis`.

This subcommand will pileup reads and then analyze SNVs, CNVs, and Tumor purity.

```
Usage: java -jar karkinos.jar analysis -n <arg> -t <arg> -r <arg> -snp <arg> -ct
       <arg> -o <arg> -id <arg> [-prop <arg>] [-mp <arg>] [-g1000 <arg>]
       [-cosmic <arg>] [-g1000freq <arg>] [-chr <arg>] [-rs <arg>] [-rg
       <arg>] [-exonSNP <arg>] [-nopdf]
 -n,--normalBam <arg>                normal BAM file
 -t,--tumorBam <arg>                 tumor BAM file
 -r,--reference <arg>                reference genome file of 2bit format
 -snp,--dbSNP <arg>                  dbSNP list (e.g. bin, chr, start, end)
 -ct,--captureTarget <arg>           BED file of capture target regions
 -o,--outdir <arg>                   output directory
 -id,--uniqueid <arg>                unique id for this sample
 -prop,--property <arg>              karkinos.property file
 -mp,--mappability <arg>             (optional) Big Wig format file of mappability from UCSC
 -g1000,--1000genome <arg>           (optional) 1000 genome list (e.g.  chr, pos, ref, alt, freq, id)
 -cosmic,--cosmicSNV <arg>           VCF format file of COSMIC's SNV
 -g1000freq,--1000genomefreq <arg>   (optional) threshold of 1000 genome frequency
 -chr,--chrom <arg>                  chromosome name
 -rs,--readsStats <arg>              (optional) reads stats files (normal and tumor)
 -rg,--refFlatGenes <arg>            (optional) gene references
 -exonSNP,--exonSNP <arg>            (optional) additional exon SNPs
 -nopdf,--nopdf                      if you don't need a graphical summary PDF
```

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