User: Peter Chung

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Peter Chung80
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80
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Location:
Hong Kong
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2 days, 13 hours ago
Joined:
3 years, 3 months ago
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q*************@gmail.com

Posts by Peter Chung

<prev • 19 results • page 1 of 2 • next >
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Comment: C: Haplotype resolving (phasing) from BAM file
... Hi, Did you solve the problem? ...
written 7 months ago by Peter Chung80
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Comment: C: call haplotypes in GATK HaplotypeCaller
... Hi finswimmer, I am using GATK4, there are not any messages but the output is 0kb. Thanks. ...
written 7 months ago by Peter Chung80
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call haplotypes in GATK HaplotypeCaller
... I am new in bioinformatics. I would like to call haplotypes in GATK HaplotypeCaller, however the output result is 0kb. Can anyone give me some advice how to do the haplotypes ? I am doing the WGS. REF="refs/ucsc.hg19.fasta" name="samples/sample-1" gatk --java-options "-Xmx16g" Haplotyp ...
haplotypecaller gatk haplotype sequencing written 7 months ago by Peter Chung80
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ides capp-seq bioinformatics pipeline
... I am new in bioinformatics. we would like to apply the iDES-enhanced CAPP-Seq (CAncer Personalized Profiling by deep Sequencing), however, I have few questions about the procedures after read those papers. I sincerely wish someone can help me for this. > capp-seq paper: https://www.ncbi.nlm.nih. ...
bioinformatics ctdna sequence snp written 8 months ago by Peter Chung80
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gatk4 GenomicsDBImport intervals with whole genome
... I am new in gatk tools, I would like to use GenomicsDBImport to merge GVCFs from multiple samples with whole genome. -L interval is a required option for GenomicsDBImport. For example, -L chr20 for contig chr20. -L chr20:1-100 for contig chr20, positions 1-100. However, I would like to import whol ...
gatk intervals genomicsdbimport written 9 months ago by Peter Chung80
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Comment: C: picard markduplicate output smaller file
... oh thanks. First I used bwa to align them and then use samtools sort to sort each bam files. Afterwards, I combined all the bam files into one bam file by samtools merge. After that, I used samtools addreplacerg to add readgroup. ###bwa and samtools sort REF="/data/data/reference/refs/ ...
written 10 months ago by Peter Chung80 • updated 10 months ago by finswimmer13k
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picard markduplicate output smaller file
... I am new in WGS analysis. First, I combine all my bam files into one and it's 157GB and then add read group on it to 159GB. Then I do the picard markduplicate step by using the following code: java -Xmx8g -Djava.io.tmpdir=${TMPFILE} -jar $PICARD MarkDuplicates \ INPUT=${FILE}.addRG.bam \ ...
gatk picard markduplicates bioinformatics written 10 months ago by Peter Chung80
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gatk HaplotyperCaller bam reference
... I am new in WGS sequencing. I am working on the gatk HaplotypeCaller step. The bam file is required for calling variants. I have generated a few bam files upstream starting from bwa. I have sample1.bam, sample1.addRG.bam for add read group and sample1.addRG.mkdup.bam for remove duplicates. Therefo ...
haplotypercaller gatk bam written 12 months ago by Peter Chung80
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picard addorreplacereadgroups output issue
... I have a 189GB bam file and I need to add a readgroup in order to do downstream steps, so I used picard AddOrReplaceReadGroups to do it. Below is my command: java -Xmx8g -jar $PICARD AddOrReplaceReadGroups \ I=${name}.bam \ O=${name}.addRG.bam \ SORT_ORDER=coordinate \ RGID=${ ...
gatk readgroups picard java sequencing written 12 months ago by Peter Chung80
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use gatk phased vcf as input file of HapCut2
... I am new in sequencing analysis and would like to do haplotype blocks from the result of WGS. But I have some questions on the HAPCUT2. I generated a vcf from gatk and then I phased it using gatk ReadBackedPhasing into phased vcf. Commands below are from HAPCUT2: ./build/extractHAIRS [options ...
hapcut2 gatk vcf phasing written 19 months ago by Peter Chung80 • updated 19 months ago by RamRS25k

Latest awards to Peter Chung

Popular Question 8 months ago, created a question with more than 1,000 views. For looking for TCGA gene expression Normal Samples
Good Question 9 months ago, asked a question that was upvoted at least 5 times. For question about the impute2 output format
Popular Question 12 months ago, created a question with more than 1,000 views. For TCGA UUID change back to TCGAbarcode
Popular Question 19 months ago, created a question with more than 1,000 views. For TCGA UUID change back to TCGAbarcode
Appreciated 19 months ago, created a post with more than 5 votes. For question about the impute2 output format
Popular Question 2.2 years ago, created a question with more than 1,000 views. For TCGA UUID change back to TCGAbarcode
Popular Question 2.2 years ago, created a question with more than 1,000 views. For looking for TCGA gene expression Normal Samples
Student 2.2 years ago, asked a question with at least 3 up-votes. For question about the impute2 output format
Supporter 2.8 years ago, voted at least 25 times.

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