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5
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0
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60
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0
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GATK variant calling on multiple bam files
gatk bam written 5 days ago by User000 • 400
0
votes
0
answers
69
views
0
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genotype 0/0 if no SNPs identified by GATK
genome gatk snp baserecalibrator written 11 days ago by ZUCM • 0 • updated 6 days ago by Biostar ♦♦ 20
1
vote
1
answer
78
views
1
answer
Somatic Structure Variation on exome-seq data - pipeline recommendations?
gatk exome-seq written 12 days ago by wiki97 • 0 • updated 12 days ago by Pierre Lindenbaum ♦ 131k
0
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0
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64
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0
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Calculation of the genotype likelyhood
genotype likelihood gatk samtools written 16 days ago by vit.filippo • 50
0
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0
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78
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0
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GATK somatic CNV results
gatk cnv somatic written 18 days ago by cocchi.e89 • 110
0
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1
answer
106
views
1
answer
GATK variant calling error
variant calling gatk snp written 18 days ago by endretoth • 20 • updated 18 days ago by Pierre Lindenbaum ♦ 131k
0
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1
answer
576
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1
answer
Error in GATK GenomicsDBImport
gatk genomicsdbimport written 7 months ago by raf.marcondes • 30 • updated 18 days ago by yussab • 10
0
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0
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59
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0
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gatk haplotypecaller report a mush lower coverage than seen in alignment
haplotypecaller gatk alignment dp coverage written 19 days ago by mark.rose • 40
3
votes
1
answer
90
views
1
answer
What is "*" in the ALT field of my VCF file
vcf gatk written 24 days ago by Frédéric Bigey • 290 • updated 24 days ago by Pierre Lindenbaum ♦ 131k
1
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0
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162
views
0
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Is it pretty common to have "reverse complemented alleles" when lifting over a vcf from hg19 to hg38?
gatk picard liftover written 27 days ago by curious • 450
0
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0
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93
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0
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Genotype imputation comparison
vcf gatk imputation genotype dosages files written 4 weeks ago by alessandrorsetti • 0 • updated 4 weeks ago by genomax ♦ 91k
1
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0
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112
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0
answers
GATK gvcf file header [ALT=<ID=NON_REF]
gatk gvcf header gvcf written 4 weeks ago by BioRyder • 180
0
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0
answers
144
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0
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Empty VCF file from Mutect2 v. GATK 4.1.6.0 in tumor only mode
gatk snp written 4 weeks ago by pm2012 • 90
0
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0
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117
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0
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truth vcf NA12878.NIST reference
vcf gatk na12878 genotype picard written 4 weeks ago by speycast • 0
0
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1
answer
202
views
1
answer
BWA-MEM - Improperly Paired Reads
genome gatk next-gen alignment bwa written 4 weeks ago by mglasena • 0 • updated 4 weeks ago by genomax ♦ 91k
0
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0
answers
156
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0
answers
Error while merging multiple vcf files using Picard MergeVcfs
genome gatk picard tool snp written 4 weeks ago by nitinra • 0 • updated 4 weeks ago by Medhat ♦ 8.8k
0
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0
answers
112
views
0
answers
VCFs appear inconsistent with view of alignment
vcf gatk freebayes bbmap igv written 5 weeks ago by mark.rose • 40
4
votes
1
answer
142
views
1
answer
VariantToTable not calling HET HOM etc
gatk variantstotable written 5 weeks ago by geneart$$ • 40 • updated 5 weeks ago by RamRS ♦ 30k
0
votes
1
answer
208
views
1
answer
panel of normal files
gatk panel-of-normal hg38 mutect2 hg19 written 5 months ago by cocchi.e89 • 110 • updated 5 weeks ago by L_LANKA • 0
0
votes
0
answers
110
views
0
answers
GATK CalculateContamination - zeros in output
gatk calculatecontamination mutect2 written 5 weeks ago by wiki97 • 0
0
votes
1
answer
111
views
1
answer
Variant filtration on lowGQ values
gatk genotype filtering written 6 weeks ago by geneart$$ • 40
0
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2
answers
305
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2
answers
Error: Could not find or load main class -Xmx4g
haplotypecaller gatk xmx4g snp written 6 months ago by Adriel Rosa • 0 • updated 6 weeks ago by larryhems • 0
1
vote
1
answer
114
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1
answer
MuTect2 annotations: number of reads at the given position
gatk coverage mutect2 written 6 weeks ago by wiki97 • 0
0
votes
1
answer
151
views
1
answer
Is it possible to use VariantRecalibrator with only one sample? (90,000 MuTect2 calls)
vqsr mutect2 gatk written 7 weeks ago by wiki97 • 0
1
vote
1
answer
77
views
1
answer
CNV .vcf retrieve involved genes
vcf gatk genes cnv written 6 weeks ago by cocchi.e89 • 110
0
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0
answers
102
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0
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GATK VQSR output
gatk applyvqsr written 7 weeks ago by geneart$$ • 40
1
vote
1
answer
120
views
1
answer
convert GATK germline CNV .vcf output to .seg/.cns format to plot
vcf gatk seg cnv cns written 7 weeks ago by cocchi.e89 • 110 • updated 7 weeks ago by newbio17 • 240
0
votes
3
answers
239
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3
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GATK VariantFiltration does not filter [SOLVED]
genome gatk variantfiltration filtering snp written 7 weeks ago by romain.coppee • 0
2
votes
2
answers
3.6k
views
2
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How Do I Use Variantfiltration To Filter By Vqslod And/Or The Tranches?
vcf gatk written 8.3 years ago by Jeremy Leipzig ♦ 19k • updated 7 weeks ago by geneart$$ • 40
4
votes
1
answer
154
views
1
answer
VQSR no r file being created
gatk vqsr written 7 weeks ago by geneart$$ • 40
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