User: Peter Chung
Peter Chung • 70
- Reputation:
- 70
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- Hong Kong
- Last seen:
- 13 hours ago
- Joined:
- 2 years, 4 months ago
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Posts by Peter Chung
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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 14 hours ago by
Peter Chung • 70
• updated
12 hours ago by
finswimmer ♦ 9.0k
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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 17 hours ago by
Peter Chung • 70
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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 weeks ago by
Peter Chung • 70
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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 weeks ago by
Peter Chung • 70
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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 8 months ago by
Peter Chung • 70
• updated
8 months ago by
RamRS ♦ 20k
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... 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 ...
written 9 months ago by
Peter Chung • 70
• updated
9 months ago by
dariober ♦ 9.8k
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... 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 ...
written 18 months ago by
Peter Chung • 70
• updated
17 months ago by
Biostar ♦♦ 20
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... 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 Chung • 70
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6 follow
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... 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 ...
written 23 months ago by
Peter Chung • 70
• updated
20 months ago by
ShirleyDai • 40
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... 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 ...
written 23 months ago by
Peter Chung • 70
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