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ShujiaHuang
/ BGI_cluster.cpuinfo.txt
Last active
June 20, 2016 09:43
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| $ cat /proc/cpuinfo | |
| processor : 0 | |
| vendor_id : GenuineIntel | |
| cpu family : 6 | |
| model : 44 | |
| model name : Intel(R) Xeon(R) CPU X5650 @ 2.67GHz | |
| stepping : 2 | |
| microcode : 20 | |
| cpu MHz : 1600.000 | |
| cache size : 12288 KB |
ShujiaHuang
/ CNDB_ECS.update_err.log
Created
December 30, 2016 05:19
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| root@iZ88i9o3weiZ:~# apt-get update | |
| Err http://mirrors.aliyuncs.com trusty InRelease | |
| Err http://mirrors.aliyuncs.com trusty-security InRelease | |
| Err http://mirrors.aliyuncs.com trusty-updates InRelease | |
| Err http://mirrors.aliyuncs.com trusty-proposed InRelease | |
| Err http://mirrors.aliyuncs.com trusty-backports InRelease |
ShujiaHuang
/ gatk_bundle_and_WGS_test_data.sh
Last active
April 13, 2024 02:16
Common datasets for GATK
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| #Known datasets: GATK bundle for human b37 reference | |
| # | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/dbsnp_138.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.indels.b37.vcf.gz.md5 | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz | |
| wget -c ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37/1000G_phase1.snps.high_confidence.b37.vcf.gz.md5 |
ShujiaHuang
/ merge.py
Last active
June 19, 2023 09:43
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| def merge_region(position_region, delta=1): | |
| """Merge a batch of sorted region | |
| Parameters | |
| ---------- | |
| ``position_region``: a list like, required | |
| A regions (2D) array, format like: [[start1,end1], [start2,end2], ...] | |
| ``delta``: Integer, optinal |
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