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<prev • 567 results • page 1 of 19 • next >
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29
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No QD scores on 10% of observations in VCF?
vcf gatk qd filtering written 3 hours ago by miles.thorburn • 10
12
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178
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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 13 days ago by gaelgarcia • 100
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71
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use gatk phased vcf as input file of HapCut2
hapcut2 gatk vcf phasing written 15 days ago by Peter Chung • 70 • updated 5 days ago by Ram ♦ 15k
0
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1
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98
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1
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Calculate Depth with and without Soft-Clipping
gatk bam alignment sequencing written 7 days ago by ccnn • 0 • updated 7 days ago by Pierre Lindenbaum ♦ 107k
2
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1
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84
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1
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Can I use different versions of dbsnp for variant calling using GATK and variant annotation?
variant calling gatk dbsnp variant annotation written 8 days ago by dolevrahat • 10 • updated 8 days ago by finswimmer • 2.0k
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1
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1.1k
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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 2.3 years ago by umn_bist • 300 • updated 8 days ago by Biostar ♦♦ 20
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144
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0
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Log-odds based filtering and pairHMM alignment during local realignment
gatk mutect bayes written 9 weeks ago by CY • 130 • updated 9 days ago by Biostar ♦♦ 20
2
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1
answer
84
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1
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VariantsToBinaryPed tool missing from GATK4?
gatk4 gatk gatk3 plink king written 11 days ago by gaelgarcia05 • 170
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1
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76
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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 11 days ago by gaelgarcia05 • 170 • updated 10 days ago by Alex Reynolds ♦ 23k
2
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1
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228
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1
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Tools to check consistency between VCF genotypes and pedigree-stated sex and family relationships
vcf gatk plink snp king written 18 days ago by gaelgarcia • 100 • updated 16 days ago by chrchang523 ♦ 3.4k
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0
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78
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0
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Wrong genotype assignation in GATK?
vcf gatk genotype snp written 17 days ago by Rob • 90
3
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1
answer
272
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1
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Strategy in WGS variant calling using GATK (CombineGVCF step)
variant calling gatk snp wgs written 27 days ago by prasundutta87 • 170
2
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1
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129
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1
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How to check if BAM is indel-realigned?
gatk bam alignment indel-realignment written 27 days ago by Alice • 230
0
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1
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86
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1
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GATK gradlew bundle Error
software error gatk written 4 weeks ago by Abdul Rafay Khan • 810 • updated 4 weeks ago by dariober ♦ 9.1k
4
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2
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788
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2
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bwa mem: Passing a variable to read group
variant calling bwa-mem alignment bwa gatk written 6 months ago by rmf • 270
3
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2
answers
718
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2
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Problem parsing interval list file to GenomicsDBImport in GATK4
gatk parsing interval gvcf written 5 months ago by Yatros • 10 • updated 5 weeks ago by prnsml • 0
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2
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152
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5 follow
2
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Is indel realigning necessary for INDEL discovery?
indel gatk indelrealigner written 5 weeks ago by deepti1rao • 0 • updated 5 weeks ago by Jorge Amigo ♦ 10k
2
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1
answer
102
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1
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What's 1000 Genome indel calls??
gatk 1000genome realignertargetcreater written 5 weeks ago by 2012secondseason • 10 • updated 5 weeks ago by h.mon ♦ 14k
3
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0
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151
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0
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No mutations in BAM (IGV) but a mutation in final VCF?
variant calling gatk haplotypecaller bam igv written 5 weeks ago by mhmtgenc85 • 30 • updated 5 weeks ago by WouterDeCoster ♦ 28k
3
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0
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179
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5 follow
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Is there a easy to use GATK pipeline for SNP calling?
gatk written 6 weeks ago by Chen • 670
1
vote
1
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113
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1
answer
GATK Error on variant filteration
gatk sor filter written 6 weeks ago by deepak.k.choubey • 20 • updated 6 weeks ago by Pierre Lindenbaum ♦ 107k
2
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1
answer
166
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1
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WARN in GATK HaplotypeCaller
haplotypecaller gatk snp written 7 weeks ago by siyavash_damdar • 20 • updated 7 weeks ago by Ram ♦ 15k
0
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0
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152
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0
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InDel marker using GATK and Mummer
genome gatk mummer sequence written 7 weeks ago by anithabioinfor • 0 • updated 7 weeks ago by vdauwera • 750
1
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1
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141
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1
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GATK: .ped vs .fam and missing values
variant-calling gatk snp written 7 weeks ago by rmf • 270 • updated 7 weeks ago by Kevin Blighe ♦ 19k
9
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1
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346
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1
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Variant Calls: Freebayes vs GATK
.vcf gatk freebayes written 8 weeks ago by oars • 110 • updated 7 weeks ago by vdauwera • 750
1
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0
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126
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0
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Variant calling with GATK on human cancer samples aligned against GRCh38.p10
genome gatk next-gen alignment snp written 8 weeks ago by mihai72 • 0
1
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1
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244
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1
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Mutect2 filtering log-odds (LOD) threshold
gatk mutect written 8 weeks ago by CY • 130
2
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3
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265
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3
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Realignment disappeared in gatk4
gatk realignment written 8 weeks ago by fabbri.marco • 0 • updated 8 weeks ago by igor • 6.0k
1
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0
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127
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0
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combineVariants error for merging two vcf files
gatk combinevariants snp written 8 weeks ago by GK1610 • 30 • updated 8 weeks ago by Pierre Lindenbaum ♦ 107k
3
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1
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119
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1
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a question about HaplotypeCaller and skipping "indel realignment" and re-calibration" steps
gatk snp gvcf written 8 weeks ago by siyavash_damdar • 20 • updated 8 weeks ago by Devon Ryan ♦ 79k
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