Stephen J Newhouse

http://mrcanavar.sourceforge.net/ > mrCaNaVaR (mɪstər ʤʌnʌvʌr) is a copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the...

``` bash vt peek v0.5 description : Summarizes the variants in a VCF file usage : vt peek [options] options : -y output pdf file [summary.pdf] -x output latex directory...

https://github.com/hall-lab/speedseq/blob/master/example/example_speedseq_install.sh

### support non-freebayes/GATK callers by preprocessing https://github.com/arq5x/gemini/issues/409 https://gist.github.com/brentp/4db670df147cbd5a2b32 brentp / preprocess.py https://gist.github.com/brentp/4db670df147cbd5a2b32#file-preprocess-py

### Platypus uses its own VCF nomenclature: TC == DP, FR == AF ``` ##fileformat=VCFv4.0 ##FILTER= ##fileDate=2015-07-18 ##source=Platypus_Version_0.8.1 ##platypusOptions={'assemblyRegionSize': 1500, 'trimReadFlank': 0, 'assembleBadReads': 1, 'bamFiles': ['/home/pipeman/ngs_projects/GCAT_Data/NA12878/alignments/NA12878.WEX.100bp30x.PE.ILLUMINA.btrim.snap.hg19.filtered.bam'], 'minVarDist': 9, 'trimSoftClipped': 1,...

### Freebayes vcf header ``` ##fileformat=VCFv4.1 ##fileDate=20150719 ##source=freeBayes v0.9.21-19-gc003c1e ##reference=/home/pipeman/ngs_projects/ngseasy_resources/reference_genomes_hg19/ucsc.hg19.fasta ##phasing=none ##commandline="freebayes -f /home/pipeman/ngs_projects/ngseasy_resources/reference_genomes_hg19/ucsc.hg19.fasta -b /home/pipeman/ngs_projects/GCAT_Data/NA12878/alignments/NA12878.WEX.100bp30x.PE.ILLUMINA.no-trim.bwa.hg19.filtered.bam --min-coverage 2 --min-mapping-quality 20 --min-base-quality 20 --min-repeat-entropy 1 --genotype-qualities -- ##INFO= ##INFO= ##INFO= ##INFO=...

### ADD svtools https://github.com/hall-lab/svtools

get `http://www.ncbi.nlm.nih.gov/assembly` `http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/` `ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.15_GRCh38` `ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/README_analysis_sets.txt`

https://github.com/mozack/abra ABRA - Assembly Based ReAligner Introduction ABRA is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving...

## bam to fastq sort bam index bam then samtools?