User: Chris

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Chris40
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6 years, 11 months ago
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7 years, 1 month ago
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n*******************@yahoo.cn

Posts by Chris

<prev • 14 results • page 1 of 2 • next >
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Gatk Variantrecalibrator Is Aborted By Some Problems.
... Hi @all! It is a question about GATK VariantRecalibrator. The data I use containing 50 simples at 15X average exome sequencing. Everything seems well at the beginning. But Errors come out in the end: ERROR MESSAGE: NaN LOD value assigned. Clustering with this few variants and these annotations is ...
gatk written 6.9 years ago by Chris40 • updated 6.0 years ago by Jorge Amigo11k
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Comment: C: Samtools Depth Can Only Have Stdout?
... Warm-hearted person! ...
written 6.9 years ago by Chris40
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Comment: C: Samtools Depth Can Only Have Stdout?
... Thanks a lot!!!! ...
written 6.9 years ago by Chris40
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Comment: C: Samtools Depth Can Only Have Stdout?
... Thx a lot. So simple, I am really a Novice!! ...
written 6.9 years ago by Chris40
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Samtools Depth Can Only Have Stdout?
... Hi, everyone! I want to have a look at the depth of each position in my .bam file, so, the samtools used,samtools depth my.bam, but I find I can't get the output parameter, it only output in my Terminal screen. I want a file with whole positions' depth. How can I do it? Thx! ...
depth-of-coverage samtools output written 6.9 years ago by Chris40 • updated 6.9 years ago by Pierre Lindenbaum120k
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Comment: C: The Question About Dp Value In Mutiple Samples Calculated By Ug
... Thanks for your timely reply. I have understood more about the question. And your recommendation about -nt option helps me a lot! ...
written 7.0 years ago by Chris40
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The Question About Dp Value In Mutiple Samples Calculated By Ug
... Hi, Enthusiastic people I have my data successfully local realigned, BQSR, and then UG processing. But I find that, in VCF file, the DP value is very large, several hundred, which actually each of my data only is 10x-20x average. The data consist of 50 bams. Is the dp value calculated from 50*(10-20 ...
gatk written 7.0 years ago by Chris40 • updated 5.6 years ago by Biostar ♦♦ 20
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Comment: C: How Can I Deal With 50 Very Big .Bam Files Without Rg For Snp Calling?
... Sincere thanks! So,you mean I can merge them into one sigle big bam to apply the downstream analysis, then, the 3rd question has gone. The 4th, I mean not the what is the format of vcf but the usage. For example,-T IndelRealigner [--known /path/to/indels.vcf], what if I have no known vcf file for th ...
written 7.0 years ago by Chris40
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How Can I Deal With 50 Very Big .Bam Files Without Rg For Snp Calling?
... Hi, every friends As described, I have 50 mapped big .bam files (human exome,50 individual, 3GB average) which have no RGs. So, I want to use Picard AddOrReplaceReadGroups to add RGs. The Question: 1:For each,for example, RGID=(1,2,3..50) RGLB=(Lb.1,2,3..50) ( RGPL=ILLUMINA RGSM=(Tibet1,2,3..50). I ...
gatk snp written 7.0 years ago by Chris40 • updated 7.0 years ago by Arun2.3k
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Comment: C: Why Gatk Realignertargetcreator Outputs An Empty .Intervals???
... Tnaks for the timely reply and sorry for my delay. I have download the data, hg19.20.bam and its fasta file, in GATK resource bundle b37 to check the approach. Finally, I get a very good result as same as the Given one, and the INDEL can be called. Also, the official reply to me said that it maybe c ...
written 7.1 years ago by Chris40

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Popular Question 7.1 years ago, created a question with more than 1,000 views. For Why Gatk Realignertargetcreator Outputs An Empty .Intervals???

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