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Month: September 2014
How to manage with less technical knowledge?
I’ve become a project manager in my company and here is what I’ve experienced till now:
At first, I was trying to keep in shape technically with other developers of the team (about 15 developers) …
How to manage with less technical knowledge?
I’ve become a project manager in my company and here is what I’ve experienced till now:
At first, I was trying to keep in shape technically with other developers of the team (about 15 developers) …
Managing and Motivating Developers: Tips for Management Cluefulness
Encouraging productivity from your programming staff–at least in the developers’ estimation–requires a few special techniques.
Managing and Motivating Developers: Tips for Management Cluefulness
Encouraging productivity from your programming staff–at least in the developers’ estimation–requires a few special techniques.
Seven lessons I learned from the failure of my first startup, Dinnr
(Background: Dinnr was an ad-hoc, same day ingredient delivery service. Select a recipe on our website, and we deliver e…
Seven lessons I learned from the failure of my first startup, Dinnr
(Background: Dinnr was an ad-hoc, same day ingredient delivery service. Select a recipe on our website, and we deliver e…
Report LGC
indel detection
dindel
test mpileup
./samtools-bcftools-htslib-1.0_x64-linux/bin/samtools mpileup MM140738JS.bam -v -u > test.vcf
10:72358747
samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam
./samtools-bcftools-htslib-1.0_x64-linux/bin/samtools mpileup -uf /lgc/datasets/hg19/new/hg19/hg19.fa MM140738JS.bam | ./samtools-bcftools-htslib-1.0_x64-linux/bin/bcftools call -mv > var.raw.vcf
http://gatkforums.broadinstitute.org/discussion/3255/indel-calling
https://www.broadinstitute.org/files/shared/mpg/nextgen2011/nextgen2011_delangel.pdf
GATK -glm INDEL
python /lgc/scripts/unifiergenotyper_indel.py -i MM140738JS.bam -t /lgc/datasets/sickkids/AmpliSeqExome.20131001.designed.bed -o MM140738JS.indel.vcf
grep “72358746” *.vcf [ 7:47AM]
raony@mendel{MM140738JS} grep “72358745” *.vcf [ 7:48AM]
MM140738JS.indel.vcf:chr10 72358745 . CA C 1049.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.769;DP=84;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=81.36;MQ0=0;MQRankSum=-1.613;QD=12.50;ReadPosRankSum=0.095 GT:AD:DP:GQ:PL 0/1:47,32:81:99:1087,0,1785