Get 10% of triobra1 and calculate REAP /projects/relatedness/plink-1.07-x86_64/plink –file trio1_bra.phasing –thin 0.2 –noweb –geno 0 –recode –out trio1_bra.phasing.20   /projects/relatedness/plink-1.07-x86_64/plink –file trio1_bra.phasing –thin 0.1 –noweb –geno 0 –recode –out trio1_bra.phasing.10 Of these, 956761  snps are new, 5637 already exist Cálculo só com os brasileiros merge3.ped

Report 210213

Vcf::throw(‘Vcf4_1=HASH(0x1ce37c8)’, ‘The command “tabix -l /projects/1000genomes/integrated_call_s…’) called at /lgc/programs/vcftools_0.1.10/lib/perl5/site_perl/Vcf.pm line 2630
VcfReader::get_chromosomes(‘Vcf4_1=HASH(0x1ce37c8)’) called at /lgc/programs/vcftools_0.1.10/bin/vcf-merge line 195
main::init_cols(‘HASH(0x18d5c18)’, ‘Vcf4_1=HASH(0x18dcd30)’) called at /lgc/programs/vcftools_0.1.10/bin/vcf-merge line 277
main::merge_vcf_files(‘HASH(0x18d5c18)’) called at /lgc/programs/vcftools_0.1.10/bin/vcf-merge line 12
Traceback (most recent call last):
File “/lgc/scripts/reap.py”, line 51, in

Report 10/10/12

http://watson.nci.nih.gov/bioc_mirror/packages/release/bioc/vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf

http://www.bioconductor.org/packages/2.11/bioc/manuals/GenomicFeatures/man/GenomicFeatures.pdf

http://bioconductor.org/help/course-materials/2010/SeattleIntro/GenomicFeatures.pdf

Page 6 exactly what we need.

http://www.bioconductor.org/help/course-materials/2012/BioC2012/ranges.R

http://bioconductor.org/packages/release/bioc/vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf

Report 02/10/12

Bioconductor Libraries to learn

http://www.bioconductor.org/packages/2.10/bioc/vignettes/topGO/inst/doc/topGO.pdf

Keggapi

Updated R to version 2.15

echo "deb http://cran.mirrors.hoobly.com/bin/linux/ubuntu precise/" >> /etc/apt/sources.list
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -

Installed

http://www.omegahat.org/RCurl/FAQ.html

Biomart

library(KEGGSOAP)
genes <- get.genes.by.pathway(“path:hsa04340”)
#for each gene
genes <- sub(“(hsa:)”, “”, genes)
length(genes)
genes
#biomart
library(“biomaRt”)
ensembl = useMart(“ensembl”,dataset=”hsapiens_gene_ensembl”)

goids = getBM(attributes=c(‘entrezgene’,’go_id’), filters=’entrezgene’, values=genes, mart=ensembl)

 

 

Report 21/09/12

Indel Detection

Atlas, Dindel

ruby1.9.1 /lgc/programs/Atlas2_v1.4.1/Atlas-Indel2/Atlas-Indel2.rb -b ../../input/Exome_1_RP.realigned-recalibrated.bam -r /lgc/datasets/gatk_data/hg19/ucsc.hg19.fasta -o rms_indel -S

Varid Indel

varid_exec -a ../../../../input/Exome_1_RP.realigned-recalibrated.sam -r /lgc/datasets/gatk_data/hg19/ucsc.hg19.fasta -o varid_rms_detection –threads 4 –format vcf

Phasing Beagle