I am using and PicardTools 1.117 to prep files for GATK 3.2. ReorderSam throws an exception so it may be failing to complete the output bam/bai files. 50 wrote: I have been trying to map a set of SNPs from hg38 back to hg19 based on their rsid. To achieve this, I have downloaded the dbSNP records from (will. I have used dbSNP build 138 to tag 'rs' ID in my VCF file. But later I came to know that now dbSNP build 150 has been released. I want to update the rs IDs in my VCF file. I tried but I found a problem for which I need suggestion. With dbSNP build 138, I am getting 450076 total variants, 248236 as known variants and the rest as novel. But when I use the latest dbSNP file, All_20170710.vcf.gz, I am getting same total variants but 0 as known and all as novel which is definitely wrong. When I checked the reason for this, I found that in the All_20170710.vcf.gz VCF file, all chromosomes are written as numbers like 1, 2, instead of chr1, chr2 while in my vcf file, all chromosomes are written as chr1, chr2. The dbSNP build 138 file also has the chromosome names with the chr prefix, and that's why 138th build was giving good results. One solution would be add the chr word before chromosome number. Is that an efficient way? How do I do that? If not, what is the correct way to use the latest dbSNP All_20170710.vcf.gz to tag rs IDs in a vcf file which contains ~32 Billion SNPs instead of dbsnp_138.vcf which contains only ~6 Billion SNPs? Any suggestions?? Usage: java -jar jarfile [ -h| --help] [ -v| --version] [ - H| --host[ = 127.0. 0.1]] [ -p| --port[ = 3306]] [ -u| --user[ =root]] [ - P| --pwd[ =root]] [ -d| --database[ = DNA_RNA_MODE]] [ -m| --mode[ =dnarna]] [ -i| --input] [ -o| --output[ =. Java -jar E: Workspace REFilters out artifacts REFilters REFilters_jdk1. 6.0_43.jar ^ --host = 127.0. 0.1 ^ --port = 3306 ^ --user =root ^ --pwd = 123456 ^ --mode =denovo ^ --input = D: Downloads Documents BJ22.snvs.hard.filtered.vcf, D: Downloads Documents hg19.txt, D: Downloads Documents genes.gtf, D: Downloads Documents hg19.fa.out, D: Downloads Documents dbsnp_138.hg19.vcf ^ --output = E: Workspace REFilters Results ^ --export =all ^ --r = C: R R - 3.1. 1 bin Rscript.exe • • In Windows, use '-' patterns. Java -jar E: Workspace REFilters out artifacts REFilters REFilters_jdk1. 6.0_43.jar ^ - H 127.0. 0.1 ^ -p 3306 ^ -u root ^ - P 123456 ^ -d BJ22_DNA_RNA ^ -m dnarna ^ -i D: Downloads Documents BJ22.snvs.hard.filtered.vcf, D: Downloads Documents BJ22_sites.hard.filtered.vcf, D: Downloads Documents hg19.txt, D: Downloads Documents genes.gtf, D: Downloads Documents hg19.fa.out, D: Downloads Documents dbsnp_138.hg19.vcf ^ -o E: Workspace REFilters Results ^ -e chrom,pos,level ^ -r C: R R - 3.1. 1 bin Rscript.exe • • In CentOS, use '-' and '--' patterns. Bosch manual troubleshooting. In either case, it needs to be scrubbed clean of any debris that would impede water moving through it. Soal Matematika Sd Kelas 3 Semester 2. SOAL UTS MATEMATIKA KELAS 4 SEMESTER 2.pdf. Soal Ukk Matematika Kelas 3 Sd. Kelas 3 sd semester 2 BAB Pecahan Sederhana. Kumpulan soalulangan Kelas 5, pecahan, Semester 2, soal matematika kelas 5, soal ulangan harian Edit. Dapatkan Soal ulangan uts genap matematika kelas 1 sd semester II terbaru Soal IPA Kelas 2 Sd Semester 2 Bentuk Energi dan Sumbernya 15 Soal Matematika Kelas 4 Semester 1 dan. Soal matematika sd kelas 4 semester 2 bab pecahan. BERILAH TANDA SILANG (X) PADA HURUF A, B, C ATAU D PADA JAWABAN YANG BENAR! Pada pecahan, bilangan yang berada di atas dinamakan. Dibawah ini adalah contoh soal ulangan latihan mapel matematika untuk kelas 4 sd/mi semester 2/genap sebagai acuan dan bukan soal asli melainkan 15. Bentuk sederhana dari pecahan 14/24 adalah. Bilangan romawi 1.241 adalah. Berikut ini contoh soal latihan Ulangan Tengah Semester 2 mata pelajaran Matematika untuk adik-adik yang duduk di bangku Sekolah Dasar kelas 4. Berilah tanda silang ( X ) pada huruf a, b, c atau d di depan jawaban yang paling benar! Java -jar /home /seq /softWare / RED / REFilter.jar -h 127.0. 0.1 -p 3306 -u seq - P 123456 -m denovo --rnavcf = /data /rnaEditing / GM12878 / GM12878.snvs.hard.filtered.vcf --repeat = /home /seq /softWare / RED /hg19.fa.out --splice = /home /seq /softWare / RED /genes.gtf --dbsnp = /home /seq /softWare / RED /dbsnp_138.hg19.vcf --darned = /home /seq /softWare / RED /hg19.txt --r = /usr /bin / Rscript Bugs and feature requests Have a bug or a feature request? Please first read the and search for existing and closed issues. If your problem or idea is not addressed yet, please open a. Creators Xing Li • • email: Copyright and license Code and documentation copyright 2013-2014 BUPT/CQMU. REFilter is a free software, and you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.
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