User: Peter Chung

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Peter Chung70
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Hong Kong
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13 hours ago
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2 years, 4 months ago
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Posts by Peter Chung

<prev • 14 results • page 1 of 2 • next >
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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 14 hours ago by Peter Chung70 • updated 12 hours ago by finswimmer9.0k
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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 17 hours ago by Peter Chung70
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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 7 weeks ago by Peter Chung70
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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 7 weeks ago by Peter Chung70
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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 8 months ago by Peter Chung70 • updated 8 months ago by RamRS20k
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bwa mem without -M option how to continue using picard
... I do the alignment without -M option and now I have all the bam file and would like to do the downstream steps using picard and GATK, what can I do to restore the -M option except realign all the fastq because I have more than hundreds fastq files. Thank you ...
assembly sequence sequencing written 9 months ago by Peter Chung70 • updated 9 months ago by dariober9.8k
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is it .impute2 format equal to .gen format
... I would like to apply qctool software from .impute2 format to .bgen format. However, qctool -g HELLO.impute2 -og HELLO.bgen Error comes out: !! Error (genfile::BadArgumentError): In argument(s) filetype_hint="guess", inferred type = "" to function genfile::SNPDataSource::create(): Unrecognised f ...
impute2 imputation qctool written 18 months ago by Peter Chung70 • updated 17 months ago by Biostar ♦♦ 20
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Comment: C: Subsetting individuals from IMPUTE2 ref files: .hap and .legend
... I have that question too, https://www.biostars.org/p/239067/ do you know how to do it now? I would like to extract CHS CHB population out from .sample, .legend and .hap file of impute2 reference data phase3. ...
written 23 months ago by Peter Chung70
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imputation only choose one population as reference panel
... I have a gwas data to do the imputation by shapeit2 and impute2. I would like to use only east asians population in 1,000 Genomes haplotypes -- Phase 3 integrated variant set release in NCBI build 37 (hg19) coordinates from impute2 reference data: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3 ...
shapeit impute2 population gwas written 23 months ago by Peter Chung70 • updated 20 months ago by ShirleyDai40
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question about the impute2 output format
... I have a large snp data in plink format. I used shapeit2 to do the phasing steps and output file is gwas.phased.haps gwas.phased.sample which is normal. .haps file: 22 rs35416799 16869887 A G 22 rs115144709 17000277 A G 22 rs5746642 17055818 A G and then I used the gwas.phased.hap ...
gwas imputation snp written 23 months ago by Peter Chung70

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