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<prev • 483 results • page 1 of 17 • next >
3
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1
answer
111
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1
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Is there any way to generate interval list from available exome data?
exome gatk sequencing mutect2 written 5 days ago by Phoenix • 100 • updated 5 days ago by Pierre Lindenbaum ♦ 98k
0
votes
0
answers
106
views
0
answers
Strategies for calling variants in a transposon-rich genome
genome gatk snp written 16 days ago by Dave Carlson • 40
0
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0
answers
138
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0
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Badly formed genome location? GATK GenotypeGVCFs
gatk joint genotyping written 17 days ago by jtwalker • 10
2
votes
1
answer
115
views
1
answer
GaTK reverse select interval list
gatk intervallist written 18 days ago by Niek De Klein • 2.4k • updated 18 days ago by Pierre Lindenbaum ♦ 98k
0
votes
0
answers
111
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0
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small .bam files to test GATK Variant Discovery pipeline
gatk variant discovery bam small test written 19 days ago by alongalor • 0
0
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0
answers
188
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0
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Why the optimal value of BQSR intervals is 20
wgs gatk written 22 days ago by bluemonster0808 • 0
0
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0
answers
93
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0
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Picard HsMetrics on Whole Genome (no bedfile) need "HS_Penalty_20X & HS_LIBRARY_SIZE"
gatk picard written 23 days ago by Jon17 • 0
3
votes
1
answer
1.3k
views
1
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What does Picard tools cleansam and fixemate exactly do and what are the equivalents in samtools ?
picard tools samtools gatk written 19 months ago by BioinfoNovice • 80 • updated 23 days ago by lamteva.vera • 0
1
vote
1
answer
196
views
1
answer
HaplotypeCaller filter out variants covered only in one direction
variant calling gatk haplotype caller written 4 weeks ago by stanedav • 10 • updated 4 weeks ago by pfs • 20
2
votes
1
answer
228
views
1
answer
Why people use gatk v2.3.9lite?
gatk written 5 weeks ago by bluemonster0808 • 0 • updated 5 weeks ago by h.mon ♦ 8.7k
1
vote
1
answer
200
views
1
answer
Merging BAM file before running GATK or merging vcf output
vcf gatk snp written 6 weeks ago by pbigbig • 180 • updated 6 weeks ago by Lila M • 350
1
vote
1
answer
235
views
1
answer
rna seq genome coverage
gatk picard coverage rna-seq written 6 weeks ago by ea1402 • 10 • updated 6 weeks ago by geek_y ♦ 8.0k
1
vote
0
answers
162
views
0
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Filtering on MAF using the GATK?
variant filtering gatk snp filtering written 9 weeks ago by jtwalker • 10 • updated 7 weeks ago by Biostar ♦♦ 20
1
vote
1
answer
155
views
1
answer
Is GATK overestimating the heterozygous calls?
vcf gatk heterozygous snp written 8 weeks ago by biobudhan • 10 • updated 8 weeks ago by andrew.j.skelton73 • 3.7k
0
votes
0
answers
152
views
0
answers
Combine VCF files with multiple alternative alleles in GATK
gatk ngs sequencing combine variants calling written 8 weeks ago by ciemanek • 20
1
vote
1
answer
178
views
1
answer
Making a vcf file from a subset of regions from gvcf files
vcf gatk written 9 weeks ago by Floris Brenk • 790 • updated 8 weeks ago by aays • 60
2
votes
1
answer
196
views
1
answer
GATK VariantFiltration invalid expression
filtration gatk ngs variants written 9 weeks ago by ciemanek • 20 • updated 9 weeks ago by finswimmer • 430
2
votes
1
answer
191
views
1
answer
GATK variantFiltration unexpected behaviour?
gatk variant filtration snp written 9 weeks ago by jtwalker • 10
3
votes
1
answer
334
views
1
answer
GATK: SAM file doesn't have any read groups defined in the header.
gatk rna-seq written 9 weeks ago by mahnoornaseer97 • 0
6
votes
2
answers
215
views
2
answers
how to calling variants in RNAseq data from multiple samples?
variant calling gatk vc rna-seq written 10 weeks ago by Lila M • 350 • updated 9 weeks ago by Samuel Brady • 230
0
votes
0
answers
195
views
0
answers
variant calling discondordance between same sample between two run
disconcordance gatk abratio written 10 weeks ago by J.F.Jiang • 640
4
votes
2
answers
195
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2
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Feasible Annotation of 4 million unique SNPs
gatk ase snp written 10 weeks ago by serpalma.v • 10 • updated 10 weeks ago by Emily_Ensembl ♦ 13k
0
votes
0
answers
144
views
0
answers
dbsnp file for C. elegans
gatk dbsnp c. elegans variation file written 10 weeks ago by cristian • 80
1
vote
1
answer
456
views
1
answer
How to filter mutect2 VCF output?
gatk alignment snp mutect2 written 12 weeks ago by Whoknows • 590 • updated 10 weeks ago by poisonAlien • 2.4k
3
votes
1
answer
198
views
1
answer
GATK: SNP coverage too high?
gatk written 11 weeks ago by Marvin • 90 • updated 11 weeks ago by harold.smith.tarheel • 3.8k
0
votes
1
answer
386
views
1
answer
HapCUT2 using GATK results
hapcut2 gatk vcf phasing written 8 months ago by jyu429 • 120 • updated 11 weeks ago by lloydlow • 0
0
votes
0
answers
168
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0
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simulating variants with specific frequency using GATK
vcf gatk written 3 months ago by christacaggiano • 20 • updated 11 weeks ago by Biostar ♦♦ 20
3
votes
1
answer
225
views
1
answer
snpEff database to annotate b37 GATK output
gatk snpeff written 5 months ago by Helene • 390 • updated 3 months ago by hns • 130
2
votes
1
answer
203
views
1
answer
How to only show SNPs in vcf files
vcf gatk snp written 3 months ago by Joe • 30 • updated 3 months ago by Pierre Lindenbaum ♦ 98k
0
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0
answers
195
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0
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VCFtools intersect vs. GATK intersect
vctfools gatk intersect snp sequencing written 3 months ago by ciemanek • 20 • updated 3 months ago by Pierre Lindenbaum ♦ 98k
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