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1
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2
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106
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5 follow
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Removing Duplicates before aligning
gatk dna-seq next-gen written 18 hours ago by newbinf • 0 • updated 10 hours ago by gb • 160
0
votes
0
answers
49
views
0
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Mutect2 t_depth not matching total reads
sequencing gatk next-gen snp mutect2 written 21 hours ago by juara • 10
0
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0
answers
37
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0
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GATK Interval list for processing mouse genome WGS
genome gatk grcm38 wgs written 1 day ago by husensofteng • 0
0
votes
1
answer
136
views
1
answer
GATK errors with RealignerTargetCreator and IndelRealignment
software error gatk written 3 days ago by KG • 0
0
votes
0
answers
101
views
0
answers
Why not simple Gaussian model instead of Gaussian mixture for VQSR?
vqsr gatk written 6 weeks ago by CY • 140 • updated 2 days ago by Biostar ♦♦ 20
4
votes
2
answers
81
views
2
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Size different between two uBam file which generate from the same Fastq.
gatk bam samtools written 8 days ago by weichi • 10 • updated 8 days ago by h.mon ♦ 16k
0
votes
1
answer
104
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1
answer
Read group information
gatk picard read group bwa written 11 days ago by bwczech • 0 • updated 11 days ago by WouterDeCoster ♦ 30k
2
votes
2
answers
833
views
2
answers
GBS SNPs calling
fast-gbs gatk snp calling samtools gbs written 17 months ago by shinken123 • 50 • updated 14 days ago by Arthur Melo • 0
14
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3
answers
538
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12 follow
3
answers
How to get sample names and genotype for SNP in multi-sample VCF file
gatk genotype snp written 5 months ago by hellbio • 320 • updated 18 days ago by Pierre Lindenbaum ♦ 110k
1
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1
answer
164
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1
answer
Merging public vcf files: <NON_REF> in ALT
vcf gatk bcf written 24 days ago by jimkozubek • 20
0
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0
answers
94
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0
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2/50 inidividuals show missing data at almost all positions in final vcf generated using HaplotypeCaller
vcf gatk haplotypecaller missingdata written 25 days ago by shreyasibiswas88 • 30
1
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0
answers
67
views
0
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Input for VariantsToBinaryPed
gatk plink written 28 days ago by archie • 50 • updated 28 days ago by zx8754 ♦ 4.6k
2
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1
answer
151
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1
answer
BQSR vs VQSR
gatk snp written 5 weeks ago by James Reeve • 10 • updated 4 weeks ago by finswimmer ♦ 3.6k
0
votes
0
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93
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0
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Variant analysis on 1 or 2 samples: are the final steps of the GATK pipeline unneccessary?
gatk pipeline snp variant analysis written 5 weeks ago by YaGalbi • 1.3k
2
votes
1
answer
104
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1
answer
HaplotypeCaller output - All records are non-variant - Have I gone wrong somewhere?
haplotypecaller non_ref snp gatk written 5 weeks ago by YaGalbi • 1.3k
6
votes
1
answer
265
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1
answer
Allele Depth (AD) / Allele Balance (AB) Filtering in GATK 4
gatk allele depth filtering sequencing written 5 weeks ago by maegsul • 110 • updated 5 weeks ago by Pierre Lindenbaum ♦ 110k
0
votes
1
answer
138
views
1
answer
GATK SNPs calling multiple sample without any known SNPs database
gatk multiple-sample bsqr snp written 6 weeks ago by deepkumar1983 • 40 • updated 6 weeks ago by YaGalbi • 1.3k
1
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2
answers
470
views
2
answers
GATK HaolotypeCaller takes too much time for variant calling
haplotypecaller gatk long written 7 months ago by J.F.Jiang • 700 • updated 6 weeks ago by YaGalbi • 1.3k
2
votes
0
answers
199
views
0
answers
combineVariants error for merging two vcf files
gatk combinevariants snp written 3 months ago by GK1610 • 30 • updated 7 weeks ago by Biostar ♦♦ 20
0
votes
0
answers
94
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0
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No QD scores on 10% of observations in VCF?
vcf gatk qd filtering written 8 weeks ago by miles.thorburn • 10
12
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0
answers
357
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0
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Converting VCF to PLINK .bed binary fileset to check for pedigree errors with KING: How do conversion tools make the PLINK .fam file, without asking for family relationships a priori?
vcf fam gatk vcftools plink written 9 weeks ago by gaelgarcia • 100
0
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0
answers
146
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0
answers
use gatk phased vcf as input file of HapCut2
hapcut2 gatk vcf phasing written 10 weeks ago by Peter Chung • 70 • updated 8 weeks ago by Ram ♦ 15k
0
votes
1
answer
146
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1
answer
Calculate Depth with and without Soft-Clipping
gatk bam alignment sequencing written 9 weeks ago by ccnn • 0 • updated 9 weeks ago by Pierre Lindenbaum ♦ 110k
2
votes
1
answer
133
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1
answer
Can I use different versions of dbsnp for variant calling using GATK and variant annotation?
variant calling gatk dbsnp variant annotation written 9 weeks ago by dolevrahat • 10 • updated 9 weeks ago by finswimmer ♦ 3.6k
4
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1
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1.2k
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1
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[ERROR] Malformed VCF: empty alleles are not permitted in VCF records
vcf gatk rna-seq written 2.4 years ago by umn_bist • 310 • updated 9 weeks ago by Biostar ♦♦ 20
0
votes
0
answers
187
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0
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Log-odds based filtering and pairHMM alignment during local realignment
gatk mutect bayes written 3 months ago by CY • 140 • updated 9 weeks ago by Biostar ♦♦ 20
2
votes
1
answer
169
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1
answer
VariantsToBinaryPed tool missing from GATK4?
gatk4 gatk gatk3 plink king written 9 weeks ago by gaelgarcia05 • 180
0
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1
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131
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1
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Adjust ulimit open file handle limit on Mac OS X Sierra for GATK
gatk gatk3 macosx unix ulimit written 9 weeks ago by gaelgarcia05 • 180 • updated 9 weeks ago by Alex Reynolds ♦ 24k
2
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1
answer
303
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1
answer
Tools to check consistency between VCF genotypes and pedigree-stated sex and family relationships
vcf gatk plink snp king written 10 weeks ago by gaelgarcia • 100 • updated 10 weeks ago by chrchang523 ♦ 3.6k
0
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0
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107
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0
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Wrong genotype assignation in GATK?
vcf gatk genotype snp written 10 weeks ago by Rob • 90
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