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Comment: Comment: capmq and verifybamid
4 months ago by Peter Chung ▴ 210
0
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2
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481
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capmq and verifybamid
bam capmq vcf verifyBAMID
4 months ago by Peter Chung ▴ 210
0
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1
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462
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verifyBAMID in snakemake script error
config snakemake bam vcf verifyBAMID
updated 9 months ago by ▴ 870 • written 9 months ago by ▴ 210
1
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0
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4.3k
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Comment: Comment: Haplotype resolving (phasing) from BAM file
10 months ago by Peter Chung ▴ 210
0
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1
reply
824
views
GATK GenomicsDBImport update database error using snakemake
GenomicsDBImport snakemake gatk
updated 11 months ago by 23k • written 11 months ago by ▴ 210
0
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1
reply
546
views
Nextflow docker: Error response from daemon
sarek gatk4 docker nextflow
updated 13 months ago by 166k • written 13 months ago by ▴ 210
1
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0
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6.6k
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Comment: Comment: is it .impute2 format equal to .gen format
4.1 years ago by Peter Chung ▴ 210
1
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0
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6.6k
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Comment: Comment: is it .impute2 format equal to .gen format
4.1 years ago by Peter Chung ▴ 210
8
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12
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6.6k
views
is it .impute2 format equal to .gen format
imputation impute2 qctool
updated 4.1 years ago by ▴ 40 • written 7.9 years ago by ▴ 210
0
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0
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3.7k
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Comment: Comment: Snakemake how to use glob_wilcards properly
4.2 years ago by Peter Chung ▴ 210
1
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2
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3.7k
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Snakemake how to use glob_wilcards properly
glob wildcards snakemake python
4.2 years ago by Peter Chung ▴ 210
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0
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1.8k
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Answer: A: from phased SNPs to haplotype blocks (or phase sets)
4.3 years ago by Peter Chung ▴ 210
0
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2
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2.4k
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use gatk phased vcf as input file of HapCut2
HapCut2 gatk phasing vcf
4.3 years ago by Peter Chung ▴ 210
0
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0
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2.4k
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Comment: A: use gatk phased vcf as input file of HapCut2
4.3 years ago by Peter Chung ▴ 210
2
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0
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1.9k
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Answer: A: hapcut2 output and figures
4.3 years ago by Peter Chung ▴ 210
0
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0
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3.0k
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Comment: C: paired-end fastq file remove mismatching lengths of bases and qualities error
4.5 years ago by Peter Chung ▴ 210
0
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3
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3.0k
views
paired-end fastq file remove mismatching lengths of bases and qualities error
bbtools fastq reformat repair
updated 4.5 years ago by 102k • written 4.5 years ago by ▴ 210
6
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2
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5.0k
views
question about the impute2 output format
gwas snp imputation
updated 4.8 years ago by 89k • written 8.3 years ago by ▴ 210
2
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1
reply
5.7k
views
Answer: A: snakemake output directory
5.0 years ago by Peter Chung ▴ 210
4
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7
replies
5.7k
views
snakemake output directory
snakemake ngs
updated 14 months ago by • 0 • written 5.0 years ago by ▴ 210
0
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1
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5.7k
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Comment: C: snakemake output directory
5.0 years ago by Peter Chung ▴ 210
0
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1
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5.7k
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Comment: C: snakemake output directory
5.0 years ago by Peter Chung ▴ 210
0
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1
reply
1.9k
views
Comment: C: gatk collectallelic counts error
5.1 years ago by Peter Chung ▴ 210
0
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1
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1.9k
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Comment: C: gatk collectallelic counts error
5.1 years ago by Peter Chung ▴ 210
0
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0
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1.9k
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Comment: C: gatk collectallelic counts error
5.1 years ago by Peter Chung ▴ 210
0
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1
reply
1.9k
views
Comment: C: gatk collectallelic counts error
5.1 years ago by Peter Chung ▴ 210
1
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8
replies
1.9k
views
gatk collectallelic counts error
gatk java
5.1 years ago by Peter Chung ▴ 210
1
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1
reply
4.3k
views
Comment: C: Haplotype resolving (phasing) from BAM file
5.1 years ago by Peter Chung ▴ 210
0
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1
reply
1.9k
views
Comment: C: ctDNAtools: an R package to work with ctDNA sequencing data
5.3 years ago by Peter Chung ▴ 210
0
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1
reply
2.5k
views
ides capp-seq bioinformatics pipeline
sequence SNP ctDNA
updated 2.1 years ago by 45k • written 6.2 years ago by ▴ 210
9
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2
replies
9.5k
views
gatk4 GenomicsDBImport intervals with whole genome
gatk intervals GenomicsDBImport
updated 5.5 years ago by 48k • written 6.3 years ago by ▴ 210
0
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1
reply
4.3k
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Comment: C: Haplotype resolving (phasing) from BAM file
6.2 years ago by Peter Chung ▴ 210
0
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1
reply
1.7k
views
Comment: C: call haplotypes in GATK HaplotypeCaller
6.2 years ago by Peter Chung ▴ 210
0
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3
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1.7k
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call haplotypes in GATK HaplotypeCaller
sequencing GATK Haplotype HaplotypeCaller
6.2 years ago by Peter Chung ▴ 210
0
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1
reply
3.1k
views
Comment: C: picard markduplicate output smaller file
updated 6.4 years ago by 16k • written 6.4 years ago by ▴ 210
0
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4
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3.1k
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picard markduplicate output smaller file
picard markduplicates gatk
updated 2.1 years ago by 45k • written 6.4 years ago by ▴ 210
1
vote
4
replies
1.8k
views
picard addorreplacereadgroups output issue
gatk picard readgroups sequencing java
6.5 years ago by Peter Chung ▴ 210
1
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1
reply
2.3k
views
gatk HaplotyperCaller bam reference
gatk haplotypercaller bam
6.5 years ago by Peter Chung ▴ 210
0
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3
replies
6.9k
views
TCGA UUID change back to TCGAbarcode
TCGA RNA-Seq
updated 7.1 years ago by 89k • written 8.7 years ago by ▴ 210
0
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2
replies
2.1k
views
bwa mem without -M option how to continue using picard
sequencing assembly sequence
updated 7.2 years ago by 15k • written 7.2 years ago by ▴ 210
3
votes
4
replies
3.6k
views
imputation only choose one population as reference panel
impute2 gwas population shapeit
updated 8.1 years ago by ▴ 50 • written 8.3 years ago by ▴ 210
0
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0
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3.2k
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Comment: C: Subsetting individuals from IMPUTE2 ref files: .hap and .legend
8.3 years ago by Peter Chung ▴ 210
1
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2
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2.6k
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Questions: rsem.genes.normalized. data in GDC Legacy Archive file name to identify normal and tumor samples
TCGA RNA-Seq
updated 8.6 years ago by • 0 • written 8.7 years ago by ▴ 210
0
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1
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3.7k
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Comment: C: looking for TCGA gene expression Normal Samples
8.7 years ago by Peter Chung ▴ 210
0
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3
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3.7k
views
looking for TCGA gene expression Normal Samples
genome sequence
updated 8.8 years ago by ▴ 60 • written 8.8 years ago by ▴ 210
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