Variant calls compare tools

[szilvajuhos]

To compare VCFs we can use:

• [x] http://realtimegenomics.com/products/rtg-core-non-commercial/
• [ ] https://github.com/sequencing/hap.py
• [ ] https://github.com/bioinformed/vgraph
• [x] http://smash.cs.berkeley.edu/rescue.html (SMaSH)
• [ ] https://github.com/pelinakan/VCF_Comparisons

[szilvajuhos]

Cleaned up VCF_Comparison till the level that it can be compiled

[szilvajuhos]

• GIAB reference: http://smash.cs.berkeley.edu/data/ampx-smash-sampled-human-na12878/true.vcf
• 1KG trio reference: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20140625_high_coverage_trios_broad/CEU.wgs.consensus.20131118.snps_indels.high_coverage_pcr_free_v2.genotypes.vcf.gz https://www.biostars.org/p/133593/
• Platinum reference: ftp://platgene_ro@ussd-ftp.illumina.com/2016-1.0/hg19/small_variants/NA12878/NA12878.vcf.gz
• SMaSH reference: http://smash.cs.berkeley.edu/datasets.html