User: Peter Chung
Peter Chung • 80
- Reputation:
- 80
- Status:
- Trusted
- Location:
- Hong Kong
- Last seen:
- 23 hours ago
- Joined:
- 2 years, 10 months ago
- Email:
- q*************@gmail.com
Posts by Peter Chung
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... Hi, Did you solve the problem? ...
written 3 months ago by
Peter Chung • 80
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... Hi finswimmer,
I am using GATK4, there are not any messages but the output is 0kb.
Thanks. ...
written 3 months ago by
Peter Chung • 80
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... 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 ...
written 3 months ago by
Peter Chung • 80
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... 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. ...
written 3 months ago by
Peter Chung • 80
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... 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 ...
written 5 months ago by
Peter Chung • 80
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... 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 6 months ago by
Peter Chung • 80
• updated
6 months ago by
finswimmer ♦ 11k
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... 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 \
...
written 6 months ago by
Peter Chung • 80
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... 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 ...
written 7 months ago by
Peter Chung • 80
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... 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=${name}.addRG.bam \
SORT_ORDER=coordinate \
RGID=${ ...
written 7 months ago by
Peter Chung • 80
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... 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 ...
written 14 months ago by
Peter Chung • 80
• updated
14 months ago by
RamRS ♦ 23k
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