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3
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1
answer
1.1k
views
1
answer
best practices to use GATK with PacBio
gatk next-gen sequence snp pacbio written 2.4 years ago by Medhat ♦ 7.7k • updated 21 hours ago by prasundutta87 • 200
2
votes
0
answers
62
views
0
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Using GATK4 Mutect2 on mouse data, need a genome snp reference
vcf gatk mutect2 snp mouse written 2 days ago by jc.szamosi • 40
0
votes
0
answers
844
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0
answers
XHMM GATK exome sequencing deletions genome wide or selected genes ?
gatk genelist xhmm written 2.6 years ago by Floris Brenk • 850 • updated 4 days ago by Ram ♦ 17k
3
votes
1
answer
82
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1
answer
How can i use combination of both -nct and -nt in GATK?
genome gatk forum next-gen written 7 days ago by mandecent.gupta • 0 • updated 7 days ago by Ram ♦ 17k
1
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0
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83
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0
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Some questions about call variants for mtDNA using GATK HaplotypeCaller
haplotypecaller gatk mtdna written 16 days ago by MatthewP • 10
2
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1
answer
125
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1
answer
How to apply GATK on mtDNA sequencing data?
gatk mtdna written 21 days ago by MatthewP • 10
0
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0
answers
91
views
0
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Adam Transform BQSR result is different with Gatk
gatk bqsr adam written 24 days ago by zhangnew • 0
0
votes
0
answers
94
views
0
answers
Variant training set for Zebrafish to apply GATK VariantRecalibrator
gatk ngs zebrafish genotyping-by-sequencing snp written 4 weeks ago by Matthias • 20
0
votes
1
answer
141
views
1
answer
VCF to Bed file format using GATK
vcf gatk rna-seq bed written 4 weeks ago by Sa • 0 • updated 4 weeks ago by chrchang523 ♦ 3.9k
2
votes
1
answer
152
views
1
answer
gatk vqsr --recal-file error
gatk vqsr written 5 weeks ago by cmccabe • 170 • updated 5 weeks ago by Santosh Anand • 3.9k
2
votes
1
answer
122
views
1
answer
error using bqsr and incompatible contigs
gatk bqsr written 5 weeks ago by cmccabe • 170 • updated 5 weeks ago by h.mon ♦ 19k
1
vote
1
answer
180
views
1
answer
Hard filtering results of vcf file for multiple samps
variant calling gatk hard filtering written 6 weeks ago by seta • 1.0k • updated 6 weeks ago by finswimmer ♦ 5.3k
2
votes
1
answer
154
views
1
answer
GATK MarkDuplicates output and bam
gatk markduplicates written 6 weeks ago by cmccabe • 170 • updated 6 weeks ago by finswimmer ♦ 5.3k
0
votes
0
answers
117
views
0
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How do you get multi-allelic SNP calls form a pooled sequence using GATK?
multi-allelic_snp gatk snpcalling written 6 weeks ago by James Reeve • 30
3
votes
1
answer
166
views
1
answer
multithread support for gatk
gatk bqsr written 6 weeks ago by cmccabe • 170
0
votes
0
answers
209
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0
answers
VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
gatk written 6 weeks ago by Ana • 100 • updated 6 weeks ago by finswimmer ♦ 5.3k
4
votes
1
answer
303
views
1
answer
Locating Multiple Alternate Alleles in gatk.vcf file
vcf gatk written 6 months ago by oars • 150 • updated 7 weeks ago by Kevin Blighe ♦ 28k
1
vote
0
answers
206
views
0
answers
Adding read group to bam files from multiplexed samples
gatk picard bam written 8 weeks ago by serpalma.v • 10
2
votes
1
answer
204
views
1
answer
How to get SNV abundance in NGS analysis
gatk ngs snp written 8 weeks ago by biock • 0
1
vote
1
answer
454
views
1
answer
PINDEL and somatic mutations
gatk indelrealigned pindel written 10 months ago by Leandro de Mattos • 80 • updated 9 weeks ago by Kevin Blighe ♦ 28k
8
votes
2
answers
277
views
7 follow
2
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Removing Duplicates before aligning
gatk dna-seq next-gen written 9 weeks ago by newbinf • 0 • updated 9 weeks ago by gb • 310
0
votes
0
answers
161
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0
answers
Mutect2 t_depth not matching total reads
sequencing gatk next-gen snp mutect2 written 9 weeks ago by juara • 10
0
votes
0
answers
111
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0
answers
GATK Interval list for processing mouse genome WGS
genome gatk grcm38 wgs written 9 weeks ago by husensofteng • 10
0
votes
1
answer
232
views
1
answer
GATK errors with RealignerTargetCreator and IndelRealignment
software error gatk written 9 weeks ago by KG • 0
0
votes
0
answers
148
views
0
answers
Why not simple Gaussian model instead of Gaussian mixture for VQSR?
vqsr gatk written 3 months ago by CY • 190 • updated 9 weeks ago by Biostar ♦♦ 20
4
votes
2
answers
145
views
2
answers
Size different between two uBam file which generate from the same Fastq.
gatk bam samtools written 10 weeks ago by weichi • 10 • updated 10 weeks ago by h.mon ♦ 19k
0
votes
1
answer
198
views
1
answer
Read group information
gatk picard read group bwa written 10 weeks ago by bwczech • 0 • updated 10 weeks ago by WouterDeCoster ♦ 32k
2
votes
2
answers
981
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2
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GBS SNPs calling
fast-gbs gatk snp calling samtools gbs written 19 months ago by shinken123 • 60 • updated 11 weeks ago by Arthur Melo • 0
16
votes
3
answers
732
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13 follow
3
answers
How to get sample names and genotype for SNP in multi-sample VCF file
gatk genotype snp written 7 months ago by hellbio • 330 • updated 11 weeks ago by Pierre Lindenbaum ♦ 112k
1
vote
1
answer
270
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1
answer
Merging public vcf files: <NON_REF> in ALT
vcf gatk bcf written 12 weeks ago by jimkozubek • 20
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