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<prev • 19 results • page 1 of 1 • next >
3
votes
2
answers
132
views
2
answers
How to add "OQ" tag with read quality score as additional field in the bam file using pysam
wgs bam pysam bqsr readquality written 19 days ago by gnanakkan • 0
0
votes
0
answers
83
views
0
answers
GATK AnalyzeCovariates No improvement/Sequencing Bias Removal
gatk bqsr written 21 days ago by timothy.delory • 0
1
vote
1
answer
92
views
1
answer
Effects of applying BQSR twice?
qualityscores bqsr alignment sequencing written 5 weeks ago by Chris Miller ♦ 21k • updated 5 weeks ago by h.mon ♦ 30k
2
votes
1
answer
211
views
1
answer
BQSR Recalibration for Mycobacterium Genome Data
bqsr snp written 4 months ago by arjun.murthy779 • 10 • updated 4 months ago by 543541656 • 20
0
votes
0
answers
111
views
0
answers
is the output.table correct after BQSR?
gatk bqsr written 4 months ago by 543541656 • 20 • updated 4 months ago by Pierre Lindenbaum ♦ 129k
0
votes
0
answers
170
views
0
answers
Scatter / Gather for BaseRecalibrator on a single human WES dataset?
exome gatk next-gen human bqsr written 6 months ago by asg • 0
0
votes
0
answers
152
views
0
answers
BQSR BD/BI Tags into integer values?
gatk bqsr written 7 months ago by QVINTVS_FABIVS_MAXIMVS • 2.4k • updated 6 months ago by Biostar ♦♦ 20
0
votes
0
answers
314
views
0
answers
Population / Reference bias in GATK BQSR BaseRecalibrator?
population bias gatk bqsr non model organism written 8 months ago by Andrés Ribone • 0
1
vote
0
answers
221
views
0
answers
Any recommendations for improving Base Quality Score Recalibration (BQSR) for non-model organisms?
next-gen bqsr variant_calling written 10 months ago by elcortegano • 50
23
votes
2
answers
4.1k
views
13 follow
2
answers
BQSR: when it is applicable?
gatk bqsr base quality written 2.8 years ago by lamteva.vera • 180 • updated 12 months ago by demolidd77 • 40
8
votes
1
answer
842
views
7 follow
1
answer
FastQC before and after Base Quality Score Recalibration (BQSR)
gatk bqsr snp fastqc written 14 months ago by alicia.poppy • 50
5
votes
1
answer
1.5k
views
7 follow
1
answer
GATK quality recalibration to get recalibrated BAM files before SNP calling
gatk bqsr recalibration snp written 14 months ago by alicia.poppy • 50 • updated 14 months ago by Nicolas Rosewick ♦ 9.0k
21
votes
2
answers
2.3k
views
5 follow
2
answers
Tool: elPrep 4.0.0, a high-performance drop-in replacement tool for GATK4/Picard/SAMtools for processing SAM/BAM files
bam sam sort markduplicates bqsr tool written 21 months ago by Charlotte.Herzeel • 140
2
votes
1
answer
907
views
1
answer
error using bqsr and incompatible contigs
gatk bqsr written 24 months ago by bioguy24 • 190 • updated 18 months ago by Biostar ♦♦ 20
0
votes
0
answers
416
views
0
answers
Adam Transform BQSR result is different with Gatk
gatk bqsr adam written 23 months ago by zhangnew • 0
3
votes
1
answer
812
views
1
answer
multithread support for gatk
gatk bqsr written 2.0 years ago by bioguy24 • 190
1
vote
0
answers
1.1k
views
0
answers
GATK4 BaseRecalibrator and Target region (whole exome data)
gatk4 bqsr written 2.1 years ago by oghzzang • 40
2
votes
1
answer
1.3k
views
1
answer
Is it necessery to perform GATK-BQSR before performing variant calling using freebayes.
gatk bqsr freebayes written 3.4 years ago by sktbanerjee1 • 30 • updated 3.4 years ago by finswimmer ♦ 13k
0
votes
0
answers
1.5k
views
0
answers
BamUtil for Base Qual Recalibration
gatk bqsr basequal recalibration recal written 5.7 years ago by Danielk • 590
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