User:Lindenb/Notebook/UMR915/20110103

20101215        Top        20110104       

Bonne année !

VCFAnnotator

wrote a tool to annotate VCf files. see my blog: http://plindenbaum.blogspot.com/2011/01/my-tool-to-annotate-vcf-files.html Running this tool with belgium data.

Comparing mask/no mask

using ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/data/NA20772/sequence_read/ERR004053_*.recal.fastq.gz

mysql -D hg18 -u anonymous -e 'select distinct chrom,txStart,txEnd from knownGene where chrom="chr1" ' -N > /tmp/jeter.txt
java -jar dist/maskfasta.jar -r /tmp/jeter.txt -e 10000 /GENOTYPAGE/data/users/lindenb/MASKBWA/NO_MASK/chr1.fa >  /GENOTYPAGE/data/users/lindenb/MASKBWA/WITH_MASK/chr1.fa

[lindenb@srv-clc-02 NO_MASK]$ sed 's/N/\nN\n/g' NO_MASK/chr1.fa | grep N | wc -l
22250000
[lindenb@srv-clc-02 NO_MASK]$ sed 's/N/\nN\n/g' WITH_MASK/chr1.fa | grep N | wc -l
108399153

for each chr1.fa:

 /usr/local/package/bwa-0.5.9rc1/bwa  index  chr1.fa
 /usr/local/package/bwa-0.5.9rc1/bwa aln chr1.fa ../FASTQ/ERR004053_1.recal.fastq.gz > aln1.sai
 /usr/local/package/bwa-0.5.9rc1/bwa aln chr1.fa ../FASTQ/ERR004053_2.recal.fastq.gz > aln2.sai
 /usr/local/package/bwa-0.5.9rc1/bwa sampe chr1.fa aln1.sai aln2.sai ../FASTQ/ERR004053_1.recal.fastq.gz ../FASTQ/ERR004053_2.recal.fastq.gz > file.sam
 /usr/local/package/samtools-0.1.10/samtools faidx chr1.fa
 /usr/local/package/samtools-0.1.10/samtools view -b -t chr1.fa.fai file.sam > file.bam
 /usr/local/package/samtools-0.1.10/samtools sort file.bam sorted